Opened 5 hours ago

#19798 new defect

ChimeraX bug report submission

Reported by: jflecken@… Owned by:
Priority: normal Milestone:
Component: Unassigned Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform:
Project:

Description 

The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/jamesfleckenstein/Downloads/all-models.cxs format session

Log from Wed Jan 7 13:23:09 2026UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_1.cxs

Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #1.1, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #1.3.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #1.3.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #1.3.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #1.3.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #1.3.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #1.3.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #1.3.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #1.3.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #1.3.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #1.3.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #1.3.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #1.4,
grid size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #2.1, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #2.3.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #2.3.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #2.3.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #2.3.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #2.3.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #2.3.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #2.3.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #2.3.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #2.3.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #2.3.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #2.3.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #2.4,
grid size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as
#2.5, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values
float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #3.2.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #3.2.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #3.2.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #3.2.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #3.2.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #3.2.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #3.2.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #3.2.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #3.2.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #3.4,
grid size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as
#3.5, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values
float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3.6, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4.1, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #4.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #4.4.1, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #4.4.2, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #4.4.3, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #4.4.4, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #4.4.5, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #4.4.6, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #4.4.7, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #4.4.8, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #4.4.9, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #4.4.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #4.4.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #4.5, grid size
356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32  
Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #4.6, grid
size 356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32  
Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #4.7, grid
size 356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 0 as #4.8.1, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 1 as #4.8.2, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 2 as #4.8.3, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 3 as #4.8.4, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 4 as #4.8.5, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 5 as #4.8.6, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 6 as #4.8.7, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 7 as #4.8.8, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 8 as #4.8.9, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 9 as #4.8.10, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #4.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #4.10.1, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #4.10.2, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #4.10.3, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #4.10.4, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #4.10.5, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #4.10.6, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #4.10.7, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #4.10.8, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #4.10.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #4.10.10, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4.11, grid size 356,356,356,
pixel 0.86, shown at level 17.6, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked as #4.12, grid size
84,78,83, pixel 0.86, shown at level 12.5, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #4.13, grid
size 84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #4.14, grid
size 84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5.1, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #5.3.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #5.3.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #5.3.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #5.3.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #5.3.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #5.3.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #5.3.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #5.3.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #5.3.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #5.3.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #5.3.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6.1, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #6.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as
#6.4.1, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as
#6.4.2, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as
#6.4.3, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as
#6.4.4, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as
#6.4.5, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as
#6.4.6, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as
#6.4.7, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as
#6.4.8, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as
#6.4.9, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#6.4.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Log from Wed Jan 7 13:06:56 2026UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit2.cxs

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32  
Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32  
Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid
size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356,
pixel 0.86, shown at level 17.6, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83,
pixel 0.86, shown at level 12.5, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size
84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size
84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid
size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid
size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as
#37, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values
float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as
#38, grid size 65,50,86, pixel 0.928, shown at level 0.578, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as
#39, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values
float32  
Log from Wed Dec 10 17:24:00 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final-
> sessions\\\all-maps-aligned_Fig4-edit2.cxs

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32  
Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32  
Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid
size 78,80,66, pixel 0.928, shown at level 0.52, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356,
pixel 0.86, shown at level 17.6, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83,
pixel 0.86, shown at level 12.5, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size
84,78,83, pixel 0.86, shown at level 10.1, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size
84,78,83, pixel 0.86, shown at level 2.79, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid
size 65,50,86, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid
size 65,49,89, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as
#37, grid size 78,80,66, pixel 0.928, shown at level 0.532, step 1, values
float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as
#38, grid size 65,50,86, pixel 0.928, shown at level 0.578, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as
#39, grid size 65,49,89, pixel 0.928, shown at level 0.729, step 1, values
float32  
Log from Wed Nov 26 13:25:16 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final-
> sessions\\\all-maps-aligned_Fig4-edit2.cxs

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32  
Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32  
Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Log from Mon Nov 17 16:44:16 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final-
> sessions\\\all-maps-aligned_Fig4-edit.cxs

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
356,356,356, pixel 0.86, shown at level 0.0747, step 1, values float32  
Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
356,356,356, pixel 0.86, shown at level 0.225, step 1, values float32  
Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
356,356,356, pixel 0.86, shown at level 0.229, step 1, values float32  
Log from Sun Nov 16 18:26:26 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\David\\\Documents\\\lab\\\Berndsen\\\EatA\\\AAA_final-
> sessions\\\all-maps-aligned_Fig4-edit.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  

restore_snapshot for "ZoneColor" returned None  

Log from Sun Nov 2 23:30:54 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4.cxs

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86,
shown at level 8.74, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.152, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #22.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #22.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #22.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #22.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #22.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #22.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #22.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #22.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #22.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#22.10, grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1,
values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  
Log from Sun Nov 2 19:35:42 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned.cxs

Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.938, shown at level 0.199, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.938, shown at level 0.141, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 0.643, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.928, shown at level 1.31, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.928, shown at level 0.936, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86,
shown at level 13.2, step 1, values float32  
Log from Sun Nov 2 18:27:52 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
> maps.cxs

Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.938, shown at level 0.199, step 1, values float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.938, shown at level 0.141, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 0.643, step 1, values float32  
Opened EatA-G12_cryosparc_P6_J1227_006_volume_map_sharp.mrc as #4, grid size
352,352,352, pixel 0.86, shown at level 0.0927, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.928, shown at level 1.31, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.928, shown at level 0.936, step 1, values float32  
Log from Mon Oct 13 13:12:41 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/David/Downloads/cryosparc_P18_J419_002_volume_map_sharp.mrc
> C:/Users/David/Downloads/cryosparc_P18_J417_007_volume_map_sharp.mrc

Opened cryosparc_P18_J419_002_volume_map_sharp.mrc as #1.1, grid size
320,320,320, pixel 0.928, shown at level 0.237, step 2, values float32  
Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #1.2, grid size
320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32  

> volume #1.2 step 1

> volume #1.1 step 1

> lighting soft

> graphics silhouettes true

> volume #1.2 level 0.2819

> volume #1.1 level 0.6002

> volume #1.2 level 0.2722

> volume #1.2 level 0.4283

> volume #1.2 level 0.4965

> volume #1.2 level 0.516

[Repeated 1 time(s)]

> volume #1.1 level 0.8389

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_92/EatA-
> Fab25_RSR_real_space_refined_092.pdb

Chain information for EatA-Fab25_RSR_real_space_refined_092.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:337

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.019575,-0.54161,0.8404,72.703,-0.31976,0.79981,0.508,-15.306,-0.9473,-0.25878,-0.18884,374.61

> view matrix models
> #2,-0.021078,-0.52928,0.84819,69.83,-0.30047,0.81251,0.49955,-18.318,-0.95356,-0.24432,-0.17616,371.26

> view matrix models
> #2,-0.43727,-0.47706,0.76237,135.43,-0.29191,0.8771,0.38143,-8.1152,-0.85064,-0.055759,-0.52279,390.47

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.43727,-0.47706,0.76237,83.189,-0.29191,0.8771,0.38143,-5.8995,-0.85064,-0.055759,-0.52279,354.74

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.33831,-0.71813,0.60815,130.01,-0.57529,0.66926,0.47025,47.457,-0.7447,-0.19077,-0.63955,379.19

> view matrix models
> #2,-0.030162,-0.94176,0.33493,165.82,-0.86801,0.19083,0.45841,157.61,-0.49562,-0.27689,-0.82322,388.38

> view matrix models
> #2,-0.8649,-0.40391,-0.29801,316.37,0.11745,-0.74008,0.66218,115.68,-0.48801,0.53772,0.68753,10.919

> view matrix models
> #2,0.079061,-0.99665,0.021042,212.71,0.99636,0.078331,-0.033517,-1.4015,0.031757,0.023616,0.99922,-43.345

> view matrix models
> #2,0.70203,-0.6416,-0.30903,133.1,0.4814,0.74733,-0.45798,49.967,0.52479,0.17275,0.83352,-104.37

> view matrix models
> #2,-0.072137,-0.84932,0.52293,126.09,-0.45417,-0.43882,-0.77535,402.25,0.88799,-0.29343,-0.35408,116.36

> view matrix models
> #2,-0.24397,-0.9153,0.32049,194.43,-0.56682,-0.13357,-0.81294,381.57,0.78689,-0.37999,-0.48622,165.54

> view matrix models
> #2,-0.4587,0.70318,0.54326,-41.767,-0.50135,0.29997,-0.81158,311.26,-0.73365,-0.64464,0.21495,293.33

> view matrix models
> #2,-0.0796,0.66044,0.74665,-123.9,-0.92844,0.22354,-0.29671,292.33,-0.36286,-0.71683,0.59539,185.8

> view matrix models
> #2,-0.97691,0.040653,0.20977,181.48,-0.11542,-0.92659,-0.35793,351.21,0.17982,-0.37387,0.90988,7.3657

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.97691,0.040653,0.20977,227.65,-0.11542,-0.92659,-0.35793,345.44,0.17982,-0.37387,0.90988,63.812

> view matrix models
> #2,-0.97691,0.040653,0.20977,250.1,-0.11542,-0.92659,-0.35793,354.72,0.17982,-0.37387,0.90988,38.777

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.9871,-0.15473,0.04117,308.22,0.13002,-0.9247,-0.3578,320.19,0.093432,-0.34783,0.93289,43.18

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.9871,-0.15473,0.04117,304.34,0.13002,-0.9247,-0.3578,314.22,0.093432,-0.34783,0.93289,45.843

> view matrix models
> #2,-0.9871,-0.15473,0.04117,306.57,0.13002,-0.9247,-0.3578,317.84,0.093432,-0.34783,0.93289,55.19

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.99119,-0.13237,0.0042655,310.4,0.12491,-0.94507,-0.30205,311.75,0.044013,-0.29886,0.95328,51.664

> view matrix models
> #2,-0.98574,-0.16736,-0.017327,318.3,0.16559,-0.94674,-0.27616,301.82,0.029815,-0.2751,0.96095,48.974

> view matrix models
> #2,-0.99378,-0.11124,0.0044549,307.76,0.10846,-0.97649,-0.1863,298.4,0.025074,-0.18466,0.98248,33.191

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.99378,-0.11124,0.0044549,305.58,0.10846,-0.97649,-0.1863,296.07,0.025074,-0.18466,0.98248,30.158

> view matrix models
> #2,-0.99378,-0.11124,0.0044549,309.28,0.10846,-0.97649,-0.1863,298.31,0.025074,-0.18466,0.98248,28.351

> ui tool show "Fit in Map"

> fitmap #2 inMap #1.2

Fit molecule EatA-Fab25_RSR_real_space_refined_092.pdb (#2) to map
cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) using 5662 atoms  
average map value = 1.014, steps = 76  
shifted from previous position = 0.829  
rotated from previous position = 8.51 degrees  
atoms outside contour = 979, contour level = 0.51604  
  
Position of EatA-Fab25_RSR_real_space_refined_092.pdb (#2) relative to
cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.99740771 -0.05876321 -0.04153010 309.91242131  
0.06885727 -0.94701146 -0.31373233 322.09189835  
-0.02089356 -0.31577869 0.94860280 59.61845056  
Axis -0.01582711 -0.15960891 0.98705344  
Axis point 150.14818166 170.94658144 0.00000000  
Rotation angle (degrees) 176.29340360  
Shift along axis 2.53284185  
  

> color #1.1 #b2b2b2b4 models

> color #1.2 #ffffb2b4 models

> select clear

> show atoms

> hide #!1.1 models

> select clear

> hide #!1.2 models

> show #!1.2 models

> volume #1.2 level 0.667

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> volume #1.2 color #b2b2b2b4

> hide #!1 models

> show #!1 models

> volume #1.2 level 0.6971

> open "C:/Users/David/Downloads/cryosparc_P18_J326_007_volume_map_sharp
> (3).mrc"

Opened cryosparc_P18_J326_007_volume_map_sharp (3).mrc as #3, grid size
270,270,270, pixel 0.928, shown at level 0.253, step 2, values float32  

> volume #3 step 1

> volume #3 level 1.015

> select #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.9328,0.14313,0.33076,-50.702,-0.22451,-0.48716,0.84396,107.17,0.28193,-0.8615,-0.42229,249.44

> view matrix models
> #3,-0.73672,0.66514,-0.12179,164.83,0.31956,0.50119,0.80417,-82.828,0.59592,0.55353,-0.58179,52.47

> view matrix models
> #3,-0.85158,0.3777,-0.36353,246.42,-0.041624,0.64256,0.76511,-47.182,0.52257,0.66668,-0.53147,41.862

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.85158,0.3777,-0.36353,260.25,-0.041624,0.64256,0.76511,-31.711,0.52257,0.66668,-0.53147,92.385

> view matrix models
> #3,-0.85158,0.3777,-0.36353,258.85,-0.041624,0.64256,0.76511,-34.724,0.52257,0.66668,-0.53147,92.175

> view matrix models
> #3,-0.85158,0.3777,-0.36353,258.99,-0.041624,0.64256,0.76511,-34.078,0.52257,0.66668,-0.53147,92.512

> view matrix models
> #3,-0.85158,0.3777,-0.36353,260.01,-0.041624,0.64256,0.76511,-36.373,0.52257,0.66668,-0.53147,95.203

> view matrix models
> #3,-0.85158,0.3777,-0.36353,259.5,-0.041624,0.64256,0.76511,-35.892,0.52257,0.66668,-0.53147,96.758

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.85226,0.3822,-0.35719,258.23,-0.04208,0.63049,0.77505,-35.598,0.52143,0.67557,-0.52126,94.513

> view matrix models
> #3,-0.85502,0.39943,-0.33075,253.11,-0.043716,0.58,0.81344,-33.992,0.51675,0.70997,-0.47845,85.449

> view matrix models
> #3,-0.8535,0.39017,-0.34541,255.91,-0.04286,0.60805,0.79274,-34.956,0.51933,0.69141,-0.50224,90.421

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.8535,0.39017,-0.34541,255.05,-0.04286,0.60805,0.79274,-34.577,0.51933,0.69141,-0.50224,88.647

> view matrix models
> #3,-0.8535,0.39017,-0.34541,255.7,-0.04286,0.60805,0.79274,-33.419,0.51933,0.69141,-0.50224,86.172

> view matrix models
> #3,-0.8535,0.39017,-0.34541,259.03,-0.04286,0.60805,0.79274,-33.842,0.51933,0.69141,-0.50224,86.791

> ui tool show "Fit in Map"

> fitmap #3 inMap #1.2

Fit map cryosparc_P18_J326_007_volume_map_sharp (3).mrc in map
cryosparc_P18_J417_007_volume_map_sharp.mrc using 26648 points  
correlation = 0.9656, correlation about mean = 0.6735, overlap = 4.744e+04  
steps = 80, shift = 1.01, angle = 8.23 degrees  
  
Position of cryosparc_P18_J326_007_volume_map_sharp (3).mrc (#3) relative to
cryosparc_P18_J417_007_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.77021232 0.47584786 -0.42466666 247.21624069  
-0.05822245 0.61060460 0.78979249 -32.46293862  
0.63512448 0.63303304 -0.44259016 72.03942203  
Axis -0.13095328 -0.88532548 -0.44615023  
Axis point 115.48414946 0.00000000 89.71757642  
Rotation angle (degrees) 143.23517250  
Shift along axis -35.77391606  
  

> select clear

> hide #!2 models

> volume #3 level 0.8347

> volume #3 color #b2ffffb4

> show #!2 models

> volume #3 level 0.7072

> volume #3 color #b2b2b2b4

> select clear

> hide cartoons

> show cartoons

> select clear

> hide cartoons

> close session

[Repeated 1 time(s)]

> open C:/Users/David/Documents/lab/Berndsen/EatA/SepA/FINAL-
> MAP/cryosparc_P7_J1169_009_volume_map_sharp.mrc

Opened cryosparc_P7_J1169_009_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.938, shown at level 0.0423, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1993

> open C:/Users/David/Documents/lab/Berndsen/EatA/Pic/FINAL-
> MAP/cryosparc_P7_J1193_002_volume_map_sharp.mrc

Opened cryosparc_P7_J1193_002_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.938, shown at level 0.0447, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.1409

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab25/FINAL-
> MAP/cryosparc_P18_J417_007_volume_map_sharp.mrc

Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.6429

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/FINAL-
> MAP/cryosparc_P6_J1227_006_volume_map_sharp.mrc

Opened cryosparc_P6_J1227_006_volume_map_sharp.mrc as #4, grid size
352,352,352, pixel 0.86, shown at level 0.0202, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.09272

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab15/FINAL-
> MAP/cryosparc_P7_J1177_008_volume_map_sharp.mrc

Opened cryosparc_P7_J1177_008_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.928, shown at level 0.165, step 2, values float32  

> volume #5 step 1

> volume #5 level 1.311

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/FINAL-
> MAP/cryosparc_P7_J1175_008_volume_map_sharp.mrc

Opened cryosparc_P7_J1175_008_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.928, shown at level 0.168, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.9362

> rename #1 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc

> rename #2 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc

> hide #!3 models

> show #!3 models

> rename #3 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc

> rename #4 EatA-G12_cryosparc_P6_J1227_006_volume_map_sharp.mrc

> rename #5 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc

> hide #!5 models

> show #!5 models

> rename #6 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc

> hide #!6 models

> show #!6 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
> maps.cxs includeMaps true

——— End of log from Mon Oct 13 13:12:41 2025 ———

opened ChimeraX session  

> close #4

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/composite_map.ccp4

Opened composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at
level 1.85, step 2, values float32  

> volume #4 step 1

> volume #4 level 7.201

> volume #4 level 14.84

> rename #4 EatA-G12_composite_map.ccp4

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit map SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc in map
Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc using 38477 points  
correlation = 0.7563, correlation about mean = 0.4494, overlap = 2288  
steps = 48, shift = 0.052, angle = 0.402 degrees  
  
Position of SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) relative
to Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99997596 0.00604647 0.00339383 -1.44058630  
-0.00605023 0.99998110 0.00109714 0.77765819  
-0.00338713 -0.00111765 0.99999364 0.68143890  
Axis -0.15771004 0.48285787 -0.86138018  
Axis point 126.53476647 238.34552229 0.00000000  
Rotation angle (degrees) 0.40231685  
Shift along axis 0.01571535  
  

> fitmap #2 inMap #1

Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 35000 points  
correlation = 0.7224, correlation about mean = 0.3946, overlap = 2182  
steps = 68, shift = 0.0409, angle = 0.201 degrees  
  
Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999400 -0.00305879 -0.00162900 0.75443292  
0.00305792 0.99999518 -0.00053963 -0.38494907  
0.00163064 0.00053465 0.99999853 -0.33255063  
Axis 0.15316592 -0.46474703 0.87209541  
Axis point 125.59920279 246.17520018 0.00000000  
Rotation angle (degrees) 0.20093109  
Shift along axis 0.00444147  
  

> fitmap #3 inMap #1

Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46267 points  
correlation = 0.6022, correlation about mean = 0.3508, overlap = 8169  
steps = 96, shift = 3.11, angle = 1.41 degrees  
  
Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#3) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99955034 -0.02544878 -0.01585806 8.29018689  
0.02529220 0.99963011 -0.00999741 -0.21467164  
0.01610662 0.00959183 0.99982427 -2.08962239  
Axis 0.31050527 -0.50666621 0.80428591  
Axis point -7.00301659 313.65462831 0.00000000  
Rotation angle (degrees) 1.80764502  
Shift along axis 1.00225977  
  

> fitmap #4 inMap #1

Fit map EatA-G12_composite_map.ccp4 in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 52467 points  
correlation = 0.3705, correlation about mean = 0.1076, overlap = 9.509e+04  
steps = 268, shift = 6.78, angle = 4.91 degrees  
  
Position of EatA-G12_composite_map.ccp4 (#4) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99745944 -0.02890438 0.06510909 -9.72422277  
0.02596410 0.99862406 0.04556149 -15.05643761  
-0.06633643 -0.04375524 0.99683748 13.76545959  
Axis -0.53125257 0.78183291 0.32635565  
Axis point 209.57385733 0.00000000 174.77254945  
Rotation angle (degrees) 4.82211175  
Shift along axis -2.11316474  
  

> fitmap #5 inMap #1

Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 43899 points  
correlation = 0.3094, correlation about mean = 0.04862, overlap = 7279  
steps = 84, shift = 3.48, angle = 1.65 degrees  
  
Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#5) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99977862 -0.00827493 0.01934541 -1.34946115  
0.00863280 0.99979179 -0.01848921 3.19592240  
-0.01918838 0.01865212 0.99964189 -2.92764885  
Axis 0.66174115 0.68655052 0.30124247  
Axis point -160.69088043 0.00000000 82.25789483  
Rotation angle (degrees) 1.60812158  
Shift along axis 0.41923605  
  

> fitmap #6 inMap #1

Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 54987 points  
correlation = 0.291, correlation about mean = 0.06381, overlap = 7178  
steps = 96, shift = 4.11, angle = 1.07 degrees  
  
Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#6) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997507 -0.00632438 0.00313999 1.25675053  
0.00638150 0.99980804 -0.01852454 3.99519091  
-0.00302223 0.01854412 0.99982348 -5.71979696  
Axis 0.93448813 0.15534766 0.32031085  
Axis point 0.00000000 309.82806636 212.77029129  
Rotation angle (degrees) 1.13646017  
Shift along axis -0.03705102  
  

> select clear

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> fitmap #2 inMap #1

Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 35000 points  
correlation = 0.7223, correlation about mean = 0.3943, overlap = 2183  
steps = 44, shift = 0.00419, angle = 0.00269 degrees  
  
Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#2) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999404 -0.00305035 -0.00161912 0.74963161  
0.00304955 0.99999523 -0.00049448 -0.39244236  
0.00162062 0.00048954 0.99999857 -0.32149008  
Axis 0.14104581 -0.46437327 0.87433606  
Axis point 128.02436252 245.18440835 0.00000000  
Rotation angle (degrees) 0.19986541  
Shift along axis 0.00688177  
  

> hide #!2 models

> show #!3 models

> fitmap #3 inMap #1

Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46267 points  
correlation = 0.6024, correlation about mean = 0.3511, overlap = 8172  
steps = 48, shift = 0.0156, angle = 0.0113 degrees  
  
Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#3) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99955105 -0.02535693 -0.01595992 8.30017154  
0.02519708 0.99963109 -0.01013856 -0.18582137  
0.01621112 0.00973186 0.99982123 -2.11478903  
Axis 0.31474924 -0.50959222 0.80078005  
Axis point -8.51584380 314.90160964 0.00000000  
Rotation angle (degrees) 1.80886906  
Shift along axis 1.01368494  
  

> hide #!3 models

> show #!4 models

> fitmap #4 inMap #1

Fit map EatA-G12_composite_map.ccp4 in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 52467 points  
correlation = 0.3706, correlation about mean = 0.1079, overlap = 9.509e+04  
steps = 96, shift = 0.0067, angle = 0.0034 degrees  
  
Position of EatA-G12_composite_map.ccp4 (#4) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99746191 -0.02892500 0.06506212 -9.71065540  
0.02598869 0.99862471 0.04553325 -15.06134195  
-0.06628969 -0.04372680 0.99684183 13.75403731  
Axis -0.53119534 0.78168752 0.32679679  
Axis point 209.61127127 0.00000000 174.73954373  
Rotation angle (degrees) 4.81956456  
Shift along axis -2.12023295  
  

> volume #4 level 13.17

> show #!5 models

> select #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.99974,-0.0021662,0.022626,-2.7022,0.0025627,0.99984,-0.017509,5.4864,-0.022584,0.017563,0.99959,2.199

> fitmap #5 inMap #1

Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 43899 points  
correlation = 0.8972, correlation about mean = 0.6275, overlap = 3.444e+04  
steps = 48, shift = 1.28, angle = 1.53 degrees  
  
Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#5) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99986911 -0.01601629 -0.00228928 4.11609932  
0.01600506 0.99986019 -0.00484082 0.65293412  
0.00236649 0.00480354 0.99998566 0.36363740  
Axis 0.28563422 -0.13788868 0.94836692  
Axis point -51.09423877 231.90014067 0.00000000  
Rotation angle (degrees) 0.96733406  
Shift along axis 1.43052827  
  

> select clear

> show #!6 models

> hide #!5 models

> select #6

2 models selected  

> view matrix models
> #6,0.99998,-0.00021598,0.0064211,0.52976,0.00032798,0.99985,-0.017446,5.7292,-0.0064164,0.017448,0.99983,-1.093

> fitmap #6 inMap #1

Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 54987 points  
correlation = 0.8676, correlation about mean = 0.6394, overlap = 3.227e+04  
steps = 72, shift = 1.03, angle = 1.97 degrees  
  
Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#6) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99933723 -0.03628553 -0.00291044 7.24151640  
0.03627797 0.99933833 -0.00260875 -2.46701340  
0.00300318 0.00250144 0.99999236 0.47482860  
Axis 0.07001876 -0.08102718 0.99424945  
Axis point 68.94514654 196.03591104 0.00000000  
Rotation angle (degrees) 2.09127880  
Shift along axis 1.17903522  
  

> select clear

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned.cxs

——— End of log from Sun Nov 2 18:27:52 2025 ———

opened ChimeraX session  

> close session

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab25/FINAL-
> MAP/cryosparc_P18_J417_007_volume_map_sharp.mrc

Opened cryosparc_P18_J417_007_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.928, shown at level 0.155, step 2, values float32  

> volume #1 step 1

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab15/FINAL-
> MAP/cryosparc_P7_J1177_008_volume_map_sharp.mrc

Opened cryosparc_P7_J1177_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.928, shown at level 0.165, step 2, values float32  

> volume #2 step 1

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/FINAL-
> MAP/cryosparc_P7_J1175_008_volume_map_sharp.mrc

Opened cryosparc_P7_J1175_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.928, shown at level 0.168, step 2, values float32  

> volume #3 step 1

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/composite_map.ccp4

Opened composite_map.ccp4 as #4, grid size 356,356,356, pixel 0.86, shown at
level 1.85, step 2, values float32  

> volume #4 step 1

> open C:/Users/David/Documents/lab/Berndsen/EatA/SepA/FINAL-
> MAP/cryosparc_P7_J1169_009_volume_map_sharp.mrc

Opened cryosparc_P7_J1169_009_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.938, shown at level 0.0423, step 2, values float32  

> volume #5 step 1

> open C:/Users/David/Documents/lab/Berndsen/EatA/Pic/FINAL-
> MAP/cryosparc_P7_J1193_002_volume_map_sharp.mrc

Opened cryosparc_P7_J1193_002_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.938, shown at level 0.0447, step 2, values float32  

> volume #6 level 0.152

> volume #5 level 0.192

> volume #4 level 5.018

> volume #1 level 0.642

> volume #2 level 1.134

> volume #3 level 1.087

> select clear

> volume #4 level 8.183

> rename #1 EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc

> rename #2 EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc

> rename #3 EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc

> rename #4 EatA-G12_composite_map.ccp4

> rename #5 SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc

> rename #6 Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc

> volume #4 level 8.741

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-raw-
> maps.cxs

> ui tool show "Fit in Map"

> fitmap #1 inMap #5

Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46342 points  
correlation = 0.6022, correlation about mean = 0.3512, overlap = 8173  
steps = 68, shift = 3.08, angle = 1.81 degrees  
  
Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99955229 -0.02532125 -0.01593896 8.29155373  
0.02516068 0.99963143 -0.01019483 -0.16941286  
0.01619123 0.00978923 0.99982099 -2.12033109  
Axis 0.31676330 -0.50928889 0.80017863  
Axis point -9.22114134 314.90629443 0.00000000  
Rotation angle (degrees) 1.80764730  
Shift along axis 1.01609639  
  

> fitmap #2 inMap #5

Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 50274 points  
correlation = 0.3046, correlation about mean = 0.05393, overlap = 7630  
steps = 84, shift = 3.5, angle = 1.54 degrees  
  
Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99982218 -0.00815206 0.01700469 -0.97420968  
0.00847568 0.99978267 -0.01904684 3.32784959  
-0.01684572 0.01918758 0.99967398 -3.35959410  
Axis 0.71193720 0.63030531 0.30961367  
Axis point 0.00000000 183.69110924 160.58390930  
Rotation angle (degrees) 1.53871345  
Shift along axis 0.36380889  
  

> fitmap #3 inMap #5

Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 48158 points  
correlation = 0.2946, correlation about mean = 0.05986, overlap = 6894  
steps = 80, shift = 4.1, angle = 1.2 degrees  
  
Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99997220 -0.00682084 0.00301169 1.34581291  
0.00687870 0.99978347 -0.01963912 4.10354957  
-0.00287708 0.01965929 0.99980260 -5.91301424  
Axis 0.93495579 0.14010092 0.32592854  
Axis point 0.00000000 301.28710637 206.29677885  
Rotation angle (degrees) 1.20422719  
Shift along axis -0.09403343  
  

> fitmap #4 inMap #5

Fit map EatA-G12_composite_map.ccp4 in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 103755 points  
correlation = 0.3318, correlation about mean = 0.1473, overlap = 1.142e+05  
steps = 204, shift = 6.57, angle = 4.69 degrees  
  
Position of EatA-G12_composite_map.ccp4 (#4) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99764605 -0.02749463 0.06282048 -9.63487758  
0.02466391 0.99866437 0.04540010 -14.80531015  
-0.06398483 -0.04374383 0.99699168 13.34581636  
Axis -0.54507513 0.77535752 0.31892603  
Axis point 210.01867957 0.00000000 178.34606723  
Rotation angle (degrees) 4.69043631  
Shift along axis -1.97134816  
  

> fitmap #6 inMap #5

Fit map Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 3945 points  
correlation = 0.7433, correlation about mean = 0.3789, overlap = 272.3  
steps = 64, shift = 0.0759, angle = 0.155 degrees  
  
Position of Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999678 -0.00253741 -0.00000990 0.40619973  
0.00253740 0.99999636 -0.00091286 -0.26745975  
0.00001222 0.00091283 0.99999958 -0.17040278  
Axis 0.33851358 -0.00410176 0.94095257  
Axis point 105.67562579 162.85077747 0.00000000  
Rotation angle (degrees) 0.15450578  
Shift along axis -0.02173976  
  

> hide #!2 models

> hide #!3 models

> hide #!1 models

> hide #!6 models

> hide #!4 models

> show #!1 models

> fitmap #1 inMap #5

Fit map EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 46342 points  
correlation = 0.602, correlation about mean = 0.3509, overlap = 8170  
steps = 44, shift = 0.0169, angle = 0.00885 degrees  
  
Position of EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99955149 -0.02539753 -0.01586795 8.28316091  
0.02523949 0.99963059 -0.01008202 -0.19102707  
0.01611814 0.00967700 0.99982326 -2.10511374  
Axis 0.31329444 -0.50716422 0.80288919  
Axis point -7.96659367 313.92350093 0.00000000  
Rotation angle (degrees) 1.80707931  
Shift along axis 1.00177732  
  

> hide #!1 models

> show #!2 models

> select clear

> select #2

2 models selected  

> view matrix models
> #2,0.99982,-0.0081521,0.017005,-0.93057,0.0084757,0.99978,-0.019047,4.3701,-0.016846,0.019188,0.99967,1.3882

> fitmap #2 inMap #5

Fit map EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 50274 points  
correlation = 0.8911, correlation about mean = 0.6462, overlap = 3.537e+04  
steps = 52, shift = 1.05, angle = 1.45 degrees  
  
Position of EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99986813 -0.01607165 -0.00233017 4.13572149  
0.01606034 0.99985953 -0.00479402 0.64189318  
0.00240689 0.00475597 0.99998579 0.36476558  
Axis 0.28209163 -0.13992537 0.94912865  
Axis point -50.33000827 232.76575210 0.00000000  
Rotation angle (degrees) 0.96989764  
Shift along axis 1.42304475  
  

> select clear

> show #!3 models

> hide #!2 models

> select #3

2 models selected  

> view matrix models
> #3,0.99997,-0.0068208,0.0030117,1.6929,0.0068787,0.99978,-0.019639,5.2445,-0.0028771,0.019659,0.9998,-1.9579

> view matrix models
> #3,0.99997,-0.0068208,0.0030117,2.2648,0.0068787,0.99978,-0.019639,4.6546,-0.0028771,0.019659,0.9998,-1.9045

> fitmap #3 inMap #5

Fit map EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 48158 points  
correlation = 0.8748, correlation about mean = 0.6251, overlap = 3.162e+04  
steps = 68, shift = 0.862, angle = 1.97 degrees  
  
Position of EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) relative
to SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99933904 -0.03624170 -0.00283274 7.22320571  
0.03623384 0.99933948 -0.00277662 -2.42208705  
0.00293150 0.00267214 0.99999213 0.46175203  
Axis 0.07473445 -0.07906158 0.99406440  
Axis point 67.81464889 195.61513332 0.00000000  
Rotation angle (degrees) 2.08913166  
Shift along axis 1.19032756  
  

> select clear

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!6 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned.cxs

> volume #2 color #b2b2b2

> volume #3 color #b2b2b2

> volume #4 color #b2b2b2

> volume #5 color #b2b2b2

> volume #6 color #b2b2b2

> select clear

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned.cxs

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_207/EatA-
> Fab25_RSR_real_space_refined_207.pdb

Chain information for EatA-Fab25_RSR_real_space_refined_207.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> fitmap #7 inMap #1

Fit molecule EatA-Fab25_RSR_real_space_refined_207.pdb (#7) to map
EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) using 5662 atoms  
average map value = 1.043, steps = 76  
shifted from previous position = 3.03  
rotated from previous position = 1.83 degrees  
atoms outside contour = 1292, contour level = 0.642  
  
Position of EatA-Fab25_RSR_real_space_refined_207.pdb (#7) relative to
EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999987 -0.00006130 -0.00050676 0.09488947  
0.00006108 0.99999991 -0.00041961 0.05351513  
0.00050679 0.00041958 0.99999978 -0.13179049  
Axis 0.63500256 -0.76693948 0.09260449  
Axis point 261.40774809 0.00000000 178.39845521  
Rotation angle (degrees) 0.03785960  
Shift along axis 0.00700779  
  

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_204/EatA-
> Fab15_RSR_real_space_refined_204.pdb

Chain information for EatA-Fab15_RSR_real_space_refined_204.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> fitmap #8 inMap #2

Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms  
average map value = 0.344, steps = 64  
shifted from previous position = 3.35  
rotated from previous position = 0.828 degrees  
atoms outside contour = 7515, contour level = 1.134  
  
Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99965040 0.02151330 0.01537039 -6.45417615  
-0.02153677 0.99976713 0.00136347 2.17299353  
-0.01533748 -0.00169402 0.99988094 -1.87229403  
Axis -0.05772305 0.57974166 -0.81275313  
Axis point 12.83952609 291.75461937 0.00000000  
Rotation angle (degrees) 1.51760461  
Shift along axis 3.15404245  
  

> fitmap #8 inMap #2

Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms  
average map value = 0.3443, steps = 28  
shifted from previous position = 0.0234  
rotated from previous position = 0.0268 degrees  
atoms outside contour = 7516, contour level = 1.134  
  
Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99965171 0.02145081 0.01537268 -6.44056543  
-0.02148140 0.99976758 0.00182777 2.09728694  
-0.01532990 -0.00215736 0.99988016 -1.78470343  
Axis -0.07528901 0.58004774 -0.81109567  
Axis point 9.47181145 289.34943309 0.00000000  
Rotation angle (degrees) 1.51654235  
Shift along axis 3.14899554  
  

> select #8/A:94

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.9999,0.0053851,0.013011,-1.2078,-0.0053501,0.99998,-0.002719,2.9631,-0.013026,0.0026492,0.99991,3.3856

> fitmap #8 inMap #2

Fit molecule EatA-Fab15_RSR_real_space_refined_204.pdb (#8) to map
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) using 9396 atoms  
average map value = 2.206, steps = 52  
shifted from previous position = 0.673  
rotated from previous position = 1.52 degrees  
atoms outside contour = 2103, contour level = 1.134  
  
Position of EatA-Fab15_RSR_real_space_refined_204.pdb (#8) relative to
EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00005009 -0.00002785 0.01579925  
0.00005009 0.99999999 -0.00012423 0.02160747  
0.00002786 0.00012422 0.99999999 -0.02398416  
Axis 0.90800904 -0.20361929 0.36614035  
Axis point 0.00000000 196.51454959 175.83117461  
Rotation angle (degrees) 0.00783869  
Shift along axis 0.00116460  
  

> select clear

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!8 models

> show #!8 models

> hide #!1 models

> show #!2 models

> hide #!7 models

> hide #!8 models

> hide #!2 models

> show #!3 models

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_206/EatA-
> Fab40_RSR_real_space_refined_206.pdb

Chain information for EatA-Fab40_RSR_real_space_refined_206.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> fitmap #9 inMap #3

Fit molecule EatA-Fab40_RSR_real_space_refined_206.pdb (#9) to map
EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) using 8896 atoms  
average map value = 0.4983, steps = 96  
shifted from previous position = 3.9  
rotated from previous position = 1.53 degrees  
atoms outside contour = 6723, contour level = 1.087  
  
Position of EatA-Fab40_RSR_real_space_refined_206.pdb (#9) relative to
EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99930604 0.03206320 -0.01895747 -1.18226441  
-0.03173743 0.99934750 0.01724283 -2.74417853  
0.01949796 -0.01662920 0.99967160 0.50386631  
Axis -0.41391611 -0.46992513 -0.77964339  
Axis point -66.30254517 17.54447497 0.00000000  
Rotation angle (degrees) 2.34500008  
Shift along axis 1.38608071  
  

> select clear

> undo

[Repeated 1 time(s)]

> select #9/B:72

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view matrix models
> #9,0.99974,-0.0041289,-0.022402,1.7094,0.0044381,0.9999,0.013769,-0.80714,0.022342,-0.013865,0.99965,0.23036

> view matrix models
> #9,0.99974,-0.0041289,-0.022402,4.6226,0.0044381,0.9999,0.013769,-0.17225,0.022342,-0.013865,0.99965,-0.15439

> fitmap #9 inMap #3

Fit molecule EatA-Fab40_RSR_real_space_refined_206.pdb (#9) to map
EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) using 8896 atoms  
average map value = 2.132, steps = 56  
shifted from previous position = 0.892  
rotated from previous position = 2.34 degrees  
atoms outside contour = 1993, contour level = 1.087  
  
Position of EatA-Fab40_RSR_real_space_refined_206.pdb (#9) relative to
EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00005262 -0.00007010 0.00210688  
-0.00005261 0.99999999 0.00008658 -0.01656140  
0.00007011 -0.00008658 0.99999999 -0.00421317  
Axis -0.70273045 -0.56902882 -0.42705517  
Axis point 0.00000000 -0.61595131 127.25149200  
Rotation angle (degrees) 0.00705908  
Shift along axis 0.00974260  
  

> select clear

> hide #!9 models

> hide #!3 models

> show #!4 models

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/composite_map.pdb

Summary of feedback from opening
C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-FINAL-
MAP/composite_map.pdb  
---  
warning | Ignored bad PDB record found on line 10676  
  
Chain information for composite_map.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select #10/A:686

7 atoms, 6 bonds, 1 residue, 1 model selected  

> view matrix models #10,1,0,0,-0.035837,0,1,0,-2.5596,0,0,1,-3.415

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.99996,-0.0058184,-0.0074329,1.8538,0.0062096,0.99854,0.053736,-11.465,0.0071093,-0.05378,0.99853,2.7087

> fitmap #10 inMap #4

Fit molecule composite_map.pdb (#10) to map EatA-G12_composite_map.ccp4 (#4)
using 10667 atoms  
average map value = 12.24, steps = 96  
shifted from previous position = 4.09  
rotated from previous position = 4.57 degrees  
atoms outside contour = 4611, contour level = 8.741  
  
Position of composite_map.pdb (#10) relative to EatA-G12_composite_map.ccp4
(#4) coordinates:  
Matrix rotation and translation  
0.99998495 -0.00175123 0.00519942 -0.64123615  
0.00175732 0.99999777 -0.00116770 -0.07419770  
-0.00519737 0.00117682 0.99998580 0.55464115  
Axis 0.20894897 0.92658767 0.31269094  
Axis point 108.14433051 0.00000000 122.46368821  
Rotation angle (degrees) 0.32144573  
Shift along axis -0.02930504  
  

> select clear

> rename #10 EatA-G12_composite_map.pdb

> rename #10 EatA-G12_composite.pdb

> rename #10 EatA-G12_composite_model.pdb

> hide #10 models

> hide #!4 models

> show #!5 models

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_208/SepA-
> Fab40_RSR_real_space_refined_208.pdb

Chain information for SepA-Fab40_RSR_real_space_refined_208.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> fitmap #11 inMap #5

Fit molecule SepA-Fab40_RSR_real_space_refined_208.pdb (#11) to map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) using 9015 atoms  
average map value = 0.3748, steps = 44  
shifted from previous position = 0.0123  
rotated from previous position = 0.0204 degrees  
atoms outside contour = 1854, contour level = 0.192  
  
Position of SepA-Fab40_RSR_real_space_refined_208.pdb (#11) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00029906 -0.00012303 0.05700002  
0.00029904 0.99999994 -0.00014720 -0.01810641  
0.00012307 0.00014716 0.99999998 -0.04998960  
Axis 0.41425820 -0.34632527 0.84169410  
Axis point 74.70753495 207.47484727 0.00000000  
Rotation angle (degrees) 0.02035684  
Shift along axis -0.01219252  
  

> select clear

> hide #!5 models

> hide #!11 models

> show #!6 models

> volume #6 step 1

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_199/Pic-
> Fab40_RSR_real_space_refined_199.pdb

Chain information for Pic-Fab40_RSR_real_space_refined_199.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select clear

> fitmap #12 inMap #6

Fit molecule Pic-Fab40_RSR_real_space_refined_199.pdb (#12) to map
Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) using 8204 atoms  
average map value = 0.1913, steps = 56  
shifted from previous position = 0.0802  
rotated from previous position = 0.146 degrees  
atoms outside contour = 3282, contour level = 0.152  
  
Position of Pic-Fab40_RSR_real_space_refined_199.pdb (#12) relative to
Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999997 0.00022320 0.00014008 -0.04271191  
-0.00022318 0.99999996 -0.00015177 0.05494657  
-0.00014012 0.00015174 0.99999998 0.00566468  
Axis 0.49903799 0.46072299 -0.73395872  
Axis point 246.49551600 191.04967817 0.00000000  
Rotation angle (degrees) 0.01742292  
Shift along axis -0.00015736  
  

> select clear

> volume gaussian #4 sDev 1

Opened EatA-G12_composite_map.ccp4 gaussian as #13, grid size 356,356,356,
pixel 0.86, shown at step 1, values float32  

> volume #13 level 5.614

> volume #13 color #b2b2b2

> select clear

> volume gaussian #6 sDev 1

Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian as #14,
grid size 320,320,320, pixel 0.938, shown at step 1, values float32  

> volume #14 level 0.04989

> hide #!13 models

> hide #!12 models

> color #14 #b2b2b2ff models

> color #12 #b2b2b2ff

> select clear

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!13 models

> hide #!14 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!14 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned.cxs

> show #!12 models

> show #!11 models

> show #10 models

> hide #!13 models

> hide #!14 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> select #7,8,9,10,11,12/A:

Expected an objects specifier or a keyword  

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> select #7,8,9,10,11,12

51840 atoms, 52845 bonds, 76 pseudobonds, 7081 residues, 11 models selected  

> color (#10#!7-9,11-12 & sel) byhetero

> color (#10#!7-9,11-12 & sel) #aaffffff

> color (#10#!7-9,11-12 & sel) #ffffffff

> select clear

> select #7,8,9,10,11/A

29785 atoms, 30287 bonds, 35 pseudobonds, 4052 residues, 9 models selected  

> select #7,8,9,10,11/A:1-256

9364 atoms, 9570 bonds, 9 pseudobonds, 1267 residues, 8 models selected  

> color (#10#!7-9,11 & sel) cornflower blue

> select clear

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> color sel magenta

> select clear

> select #7,8,9,10,11/A:481-560

474 atoms, 467 bonds, 2 pseudobonds, 90 residues, 7 models selected  

> ui tool show "Color Actions"

> color sel gold

> select clear

> select #7,8,9,10,11/A:611-629

707 atoms, 727 bonds, 95 residues, 5 models selected  

> color sel #7dcdd2ff

> select clear

> select #7,8,9,10,11/A:669-699

1047 atoms, 1047 bonds, 155 residues, 5 models selected  

> color sel #ff0000ff

> select clear

> select #7,8,9,10,11/A:781-794

284 atoms, 292 bonds, 3 pseudobonds, 38 residues, 7 models selected  

> color (#10#!8-9,11 & sel) #778899ff

> select clear

> select #7,8,9,10,11/A:834-856

304 atoms, 304 bonds, 2 pseudobonds, 40 residues, 6 models selected  

> color (#10#!8-9,11 & sel) #ff69b4ff

> select clear

> select #12

8204 atoms, 8370 bonds, 23 pseudobonds, 1192 residues, 2 models selected  

> select #12/A

5739 atoms, 5840 bonds, 14 pseudobonds, 828 residues, 2 models selected  

> select #12/A:1-251

1250 atoms, 1276 bonds, 5 pseudobonds, 178 residues, 2 models selected  

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #10 models

> hide #!11 models

> show #!11 models

> select #12/A:1-313

1657 atoms, 1694 bonds, 5 pseudobonds, 240 residues, 2 models selected  

> select #12/A:1-251

1250 atoms, 1276 bonds, 5 pseudobonds, 178 residues, 2 models selected  

> color (#!12 & sel) cornflower blue

> select clear

> select #12/A:72,100,203

15 atoms, 12 bonds, 3 residues, 1 model selected  

> color sel magenta

> select clear

> select #12/A:538-618

409 atoms, 419 bonds, 57 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #12/A:611-633

148 atoms, 152 bonds, 1 pseudobond, 20 residues, 2 models selected  

> color (#!12 & sel) #7dcdd2ff

> select #12/A:672-702

221 atoms, 224 bonds, 31 residues, 1 model selected  

> color sel #ff0000ff

> select #12/A:785-797

69 atoms, 70 bonds, 1 pseudobond, 11 residues, 2 models selected  

> color (#!12 & sel) #778899ff

> select #12/A:838-863

101 atoms, 101 bonds, 1 pseudobond, 17 residues, 2 models selected  

> color (#!12 & sel) #ff69b4ff

> select clear

> show #10 models

> show #!9 models

> show #!8 models

> show #!7 models

> select #7/B

803 atoms, 824 bonds, 2 pseudobonds, 117 residues, 2 models selected  

> color (#!7 & sel) #663399ff

> select clear

> select #7/C

700 atoms, 716 bonds, 1 pseudobond, 104 residues, 2 models selected  

> color (#!7 & sel) #55ffffff

> color (#!7 & sel) #663399ff

> color (#!7 & sel) #643399ff

> color (#!7 & sel) #633399ff

> color (#!7 & sel) #613399ff

> color (#!7 & sel) #5f3399ff

> color (#!7 & sel) #5d3399ff

> color (#!7 & sel) #5c3399ff

> color (#!7 & sel) #5a3399ff

> color (#!7 & sel) #583399ff

> color (#!7 & sel) #993633ff

> color (#!7 & sel) #995533ff

> color (#!7 & sel) #337799ff

> color (#!7 & sel) #663399ff

> color (#!7 & sel) #663499ff

> color (#!7 & sel) #673499ff

> color (#!7 & sel) #673599ff

> color (#!7 & sel) #999899ff

> color (#!7 & sel) #969399ff

> color (#!7 & sel) #7b5d99ff

> color (#!7 & sel) #010101ff

> color (#!7 & sel) #08060aff

> color (#!7 & sel) #503d64ff

> color (#!7 & sel) #513d65ff

> color (#!7 & sel) #010101ff

> color (#!7 & sel) #0c090fff

> color (#!7 & sel) #7b5d99ff

> ui tool show "Color Zone"

> show #!1 models

Need to color zone map before it can be split  

> color zone #1 near #7 distance 5.57

> volume splitbyzone #1

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #10 models

> hide #!11 models

> hide #!12 models

> ui tool show "Side View"

> open
> C:/Users/David/Documents/lab/Berndsen/EatA/models/Fab25/fold_2024_09_05_14_51_fab25_fullfab_model_0.cif

Chain information for fold_2024_09_05_14_51_fab25_fullfab_model_0.cif #16  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show Matchmaker

> matchmaker #16 to #7

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker EatA-Fab25_RSR_real_space_refined_207.pdb, chain B (#7) with
fold_2024_09_05_14_51_fab25_fullfab_model_0.cif, chain A (#16), sequence
alignment score = 518.3  
RMSD between 110 pruned atom pairs is 0.701 angstroms; (across all 117 pairs:
1.160)  
  

> rename #16 AF_EatA-25_fold_2024_09_05_14_51_fab25_fullfab_model_0.cif

> select #16/A

1652 atoms, 1694 bonds, 223 residues, 1 model selected  

> color sel #663399ff

> select clear

> select #16/A

1652 atoms, 1694 bonds, 223 residues, 1 model selected  

> select #16/B

1616 atoms, 1650 bonds, 211 residues, 1 model selected  

> color sel #7b5d99ff

> select clear

> hide #!15.3 models

> show #!15.3 models

> color zone #15.3 near #16 distance 5.57

> hide #!15.1 models

> show #!15.1 models

> color zone #15.1 near #16 distance 5.57

> hide #16 models

> view

[Repeated 1 time(s)]

> hide #!15 models

> show #!15 models

> show #!7 models

> hide #!7 models

> show #!2 models

> color zone #2 near #8 distance 5.57

> select #8/b

1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected  

> select #8/B

1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected  

> color #2,15 #36558fff

> undo

> select clear

> select #8/B

1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected  

> color #2,15 #ffff7fff

> undo

> select clear

> show #!8 models

> select clear

> select #8/B

1547 atoms, 1587 bonds, 2 pseudobonds, 204 residues, 2 models selected  

> color (#!8 & sel) #36558fff

> select clear

> color zone #2 near #8 distance 5.57

> select #8/C

1583 atoms, 1617 bonds, 3 pseudobonds, 205 residues, 2 models selected  

> color (#!8 & sel) #98a8c5ff

> select clear

> color zone #2 near #8 distance 5.57

> select clear

> view

> hide #!8 models

> volume splitbyzone #2

Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  

> hide #!17 models

> show #!17 models

> hide #!15 models

> show #!15 models

> show #!4 models

> hide #!4 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!4 models

> hide #!4 models

> hide #!17 models

> show #!17 models

> hide #!15 models

> hide #!17 models

> show #!17 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!17 models

> show #!3 models

> show #!9 models

> select #9/B

1517 atoms, 1557 bonds, 2 pseudobonds, 201 residues, 2 models selected  

> color (#!9 & sel) #ecb0e1ff

> select clear

> select #9/C

1566 atoms, 1602 bonds, 3 pseudobonds, 202 residues, 2 models selected  

> color (#!9 & sel) #f7dff3ff

> color zone #3 near #9 distance 5.57

> volume splitbyzone #3

Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 0 as #18.1, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 1 as #18.2, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 2 as #18.3, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 3 as #18.4, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 4 as #18.5, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 5 as #18.6, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 6 as #18.7, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 7 as #18.8, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 8 as #18.9, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 9 as #18.10, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  
Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc 10 as #18.11, grid
size 320,320,320, pixel 0.928, shown at level 1.09, step 1, values float32  

> hide #!9 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> hide #!18 models

> show #!18 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> hide #!18 models

> show #!18 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!15 models

> hide #!15 models

> hide #!17 models

> hide #!18 models

> show #!4 models

> show #10 models

> select #10/C

1624 atoms, 1660 bonds, 210 residues, 1 model selected  

> select #10/b

1659 atoms, 1702 bonds, 220 residues, 1 model selected  

> color sel #2c514cff

> select #10/C

1624 atoms, 1660 bonds, 210 residues, 1 model selected  

> color sel #515151ff

> color sel #4e5151ff

> color sel #31514cff

> color sel #4e5151ff

> color sel #38514dff

> color sel #010202ff

> color sel #0e1413ff

> color sel #8bcac0ff

> color sel #0e1413ff

> color sel #010202ff

> color sel #010101ff

> color sel #0a0f0eff

> color sel #67968fff

> color sel #0a0f0eff

> color sel #010101ff

> color sel #080b0aff

> color sel #50756fff

> color sel #080b0aff

> color sel #010101ff

> color sel #0c1110ff

> color sel #78afa7ff

> color zone #4 near #10 distance 5.16

> color zone #4 near #10 distance 7.73

> select clear

> hide #10 models

> volume splitbyzone #4

Opened EatA-G12_composite_map.ccp4 0 as #19.1, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 1 as #19.2, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 2 as #19.3, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 3 as #19.4, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 4 as #19.5, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 5 as #19.6, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 6 as #19.7, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 7 as #19.8, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 8 as #19.9, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 9 as #19.10, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 10 as #19.11, grid size 356,356,356, pixel
0.86, shown at level 8.74, step 1, values float32  

> hide #!19 models

> show #!19 models

> show #!15 models

> show #16 models

> hide #16 models

> show #!17 models

> hide #!17 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!17 models

> lighting flat

> lighting soft

> show #!18 models

> hide #!18 models

> hide #!19 models

> hide #!17 models

> hide #!15 models

> show #!11 models

> show #!5 models

> select #11/B

1489 atoms, 1529 bonds, 2 pseudobonds, 197 residues, 2 models selected  

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!5 models

> hide #!11 models

> hide #!19.3 models

> show #!19.3 models

> color #19.3 #77ada5ff models

> color #19.3 #6d9f98ff models

> color #19.3 #5d8882ff models

> color #19.3 #66958eff models

> color #19.3 #6b9c95ff models

> color #19.3 #6ea098ff models

> hide #!19 models

> show #!5 models

> show #!11 models

> select #11/B

1489 atoms, 1529 bonds, 2 pseudobonds, 197 residues, 2 models selected  

> color (#!11 & sel) #ecb0e1ff

> select #11/C

1363 atoms, 1394 bonds, 3 pseudobonds, 177 residues, 2 models selected  

> color (#!11 & sel) #f7dff3ff

> select clear

> color zone #5 near #11 distance 5.63

> hide #!11 models

> show #!11 models

> volume splitbyzone #5

Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 0 as #20.1, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 1 as #20.2, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 2 as #20.3, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 3 as #20.4, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 4 as #20.5, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 5 as #20.6, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 6 as #20.7, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 7 as #20.8, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 8 as #20.9, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 9 as #20.10, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  
Opened SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc 10 as #20.11, grid
size 320,320,320, pixel 0.938, shown at level 0.192, step 1, values float32  

> hide #!20 models

> show #!20 models

> hide #!11 models

> hide #!20 models

> show #!6 models

> show #!12 models

> select #12/B

1324 atoms, 1361 bonds, 5 pseudobonds, 195 residues, 2 models selected  

> color (#!12 & sel) #ecb0e1ff

> select clear

> select #12/C

1141 atoms, 1169 bonds, 4 pseudobonds, 169 residues, 2 models selected  

> color (#!12 & sel) #f7dff3ff

> select clear

> color zone #6 near #12 distance 5.63

> select clear

> hide #!6 models

> show #!14 models

> color zone #14 near #12 distance 5.63

> select clear

> hide #!14 models

> show #!13 models

> hide #!12 models

> show #!4 models

> color zone #13 near #10 distance 5.16

> color zone #13 near #10 distance 8.41

> volume splitbyzone #13

Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
356,356,356, pixel 0.86, shown at level 5.61, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
356,356,356, pixel 0.86, shown at level 5.61, step 1, values float32  

> show #!6 models

> hide #!4 models

> hide #!6 models

> hide #!21 models

> show #!12 models

> show #!14 models

> color zone #14 near #12 distance 5.63

> color zone #14 near #12 distance 18.16

[Repeated 1 time(s)]

> volume splitbyzone #14

Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #22.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #22.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #22.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #22.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #22.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #22.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #22.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #22.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #22.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#22.10, grid size 320,320,320, pixel 0.938, shown at level 0.0499, step 1,
values float32  

> hide #!12 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!22 models

> show #!22 models

> show #!21 models

> close #21

> show #!19 models

> hide #!19 models

> show #!13 models

> volume #13 level 5.718

> volume #13 level 6.761

> hide #!20 models

> hide #!22 models

> volume #13 level 6.031

> show #10 models

> close #10

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/EatA-FabG12_RSR_real_space_refined_010.pdb

Chain information for EatA-FabG12_RSR_real_space_refined_010.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> fitmap #10 inMap #4

Fit molecule EatA-FabG12_RSR_real_space_refined_010.pdb (#10) to map
EatA-G12_composite_map.ccp4 (#4) using 10667 atoms  
average map value = 6.079, steps = 108  
shifted from previous position = 5.11  
rotated from previous position = 3.39 degrees  
atoms outside contour = 7317, contour level = 8.741  
  
Position of EatA-FabG12_RSR_real_space_refined_010.pdb (#10) relative to
EatA-G12_composite_map.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99908719 -0.02008723 -0.03770012 9.06831243  
0.01942262 0.99965088 -0.01791319 5.20661755  
0.03804678 0.01716460 0.99912853 -8.56741662  
Axis 0.37982306 -0.82018902 0.42781352  
Axis point 181.12453566 0.00000000 281.40187709  
Rotation angle (degrees) 2.64665903  
Shift along axis -4.49131303  
  

> select #10/A:289

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.99859,-0.046447,0.025647,-1.6035,0.045765,0.9986,0.026541,-14.883,-0.026844,-0.02533,0.99932,5.0661

> view matrix models
> #10,0.99859,-0.046447,0.025647,-1.3589,0.045765,0.9986,0.026541,-14.699,-0.026844,-0.02533,0.99932,6.1492

> fitmap #10 inMap #4

Fit molecule EatA-FabG12_RSR_real_space_refined_010.pdb (#10) to map
EatA-G12_composite_map.ccp4 (#4) using 10667 atoms  
average map value = 14.61, steps = 76  
shifted from previous position = 1.25  
rotated from previous position = 2.63 degrees  
atoms outside contour = 3617, contour level = 8.741  
  
Position of EatA-FabG12_RSR_real_space_refined_010.pdb (#10) relative to
EatA-G12_composite_map.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99999917 0.00089157 -0.00093181 0.01897248  
-0.00089133 0.99999957 0.00025755 0.08599727  
0.00093204 -0.00025672 0.99999953 -0.10459276  
Axis -0.19553376 -0.70867599 -0.67789741  
Axis point 107.68461874 0.00000000 21.57608602  
Rotation angle (degrees) 0.07534542  
Shift along axis 0.00624920  
  

> color #13 #b2b2b2b4 models

> view

> select #10

10667 atoms, 10878 bonds, 1434 residues, 1 model selected  

> color sel #ffffffff

> select clear

> select #10/A:1-256

1941 atoms, 1986 bonds, 256 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select #10/A:78,106,211

24 atoms, 22 bonds, 3 residues, 1 model selected  

> color sel magenta

> select clear

> select #10/A:481-560

402 atoms, 401 bonds, 80 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> select clear

> select #10/A:611-629

142 atoms, 146 bonds, 19 residues, 1 model selected  

> color sel #7dcdd2ff

> select #10/A:669-699

213 atoms, 213 bonds, 31 residues, 1 model selected  

> color sel #ff0000ff

> select #10/A:781-794

100 atoms, 104 bonds, 14 residues, 1 model selected  

> color sel #778899ff

> select #10/A:834-856

170 atoms, 172 bonds, 23 residues, 1 model selected  

> color sel #ff69b4ff

> select #13

2 models selected  

> select clear

> select #10/B

1659 atoms, 1704 bonds, 220 residues, 1 model selected  

> color sel #663399ff

> color sel #2c514cff

> select #10/C

1624 atoms, 1662 bonds, 210 residues, 1 model selected  

> color sel #6ea098ff

> select clear

> color zone #13 near #10 distance 5.16

> color zone #13 near #10 distance 10.13

> color zone #13 near #10 distance 7.12

> color zone #13 near #10 distance 7.51

> color zone #13 near #10 distance 12.16

> hide #10 models

> volume #13 level 6.949

> volume #13 level 4.296

> show #!20 models

> hide #!20 models

> show #!20 models

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> volume splitbyzone #13

Opened EatA-G12_composite_map.ccp4 gaussian 0 as #21.1, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #21.2, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #21.3, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #21.4, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #21.5, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #21.6, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #21.7, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #21.8, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #21.9, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #21.10, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #21.11, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  

> open 5J44

5j44 title:  
Crystal structure of the Secreted Extracellular protein A (SepA) from Shigella
flexneri [more info...]  
  
Chain information for 5j44 #23  
---  
Chain | Description | UniProt  
A B | Serine protease SepA autotransporter | D2AJC0_SHIF2 1-1033  
  
Non-standard residues in 5j44 #23  
---  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
  
5j44 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select #23/B

7507 atoms, 7628 bonds, 1013 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="EPE"::name="HOH"

27 atoms, 15 bonds, 13 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> ui tool show Matchmaker

> matchmaker #23 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#9) with 5j44,
chain A (#23), sequence alignment score = 2951.1  
RMSD between 757 pruned atom pairs is 0.589 angstroms; (across all 769 pairs:
1.473)  
  

> hide #23 models

> hide #!21 models

> show #23 models

> show #!18 models

> hide #!18 models

> select #10/A:1-256

1941 atoms, 1986 bonds, 256 residues, 1 model selected  

> select #21

23 models selected  

> show #23 surfaces

> color #23 #ffffffff

> select #21/A:1-256

Nothing selected  

> select #23/A:1-256

1928 atoms, 1969 bonds, 256 residues, 1 model selected  

> color (#!23 & sel) cornflower blue

> select clear

> select #23/A:78,106,211

24 atoms, 22 bonds, 3 residues, 1 model selected  

> color (#!23 & sel) magenta

> select clear

> select #23/A:481-560

621 atoms, 633 bonds, 80 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> select #23/A:611-629

143 atoms, 147 bonds, 19 residues, 1 model selected  

> color (#!23 & sel) #7dcdd2ff

> select #23/A:669-699

213 atoms, 213 bonds, 31 residues, 1 model selected  

> color (#!23 & sel) #ff0000ff

> select #23/A:781-794

105 atoms, 108 bonds, 14 residues, 1 model selected  

> color (#!23 & sel) #778899ff

> select #23/A:834-856

165 atoms, 167 bonds, 23 residues, 1 model selected  

> color (#!23 & sel) #ff69b4ff

> select clear

> show #!22 models

> show #!21 models

> show #!20 models

> close #19

> show #!18 models

> show #!17 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!22 models

> show #!23 models

> hide #!23 models

> show #!15 models

> view

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!18 models

> show #!23 models

> hide #!17 models

> show #!22 models

> show #!21 models

> show #!20 models

> show #!18 models

> show #!17 models

> show #16 models

> hide #16 models

> show #!15 models

> show #16 models

> hide #16 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4.cxs

——— End of log from Sun Nov 2 19:35:42 2025 ———

opened ChimeraX session  

> show #16 models

> save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
> height 2500

> save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
> height 2600

> hide #16 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!18 models

> hide #!17 models

> hide #!15 models

> save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
> height 2500

> hide #!23 models

> show #!15 models

> save C:\Users\David/Desktop/new-snaps/EatA-25.png supersample 4 width 3000
> height 2500

> save C:\Users\David/Desktop/new-snaps/EatA-25.png supersample 4 width 3000
> height 2600

> hide #!15 models

> show #!23 models

> save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
> height 2600

> hide #!23 models

> show #!17 models

> save C:\Users\David/Desktop/new-snaps/EatA-15.png supersample 4 width 3000
> height 2600

> hide #!17 models

> show #!18 models

> save C:\Users\David/Desktop/new-snaps/EatA-40.png supersample 4 width 3000
> height 2600

> hide #!18 models

> show #!20 models

> save C:\Users\David/Desktop/new-snaps/SepA-40.png supersample 4 width 3000
> height 2600

> hide #!20 models

> show #!21 models

> save C:\Users\David/Desktop/new-snaps/EatA-G12.png supersample 4 width 3000
> height 2600

> show #!22 models

> hide #!21 models

> save C:\Users\David/Desktop/new-snaps/Pic-40.png supersample 4 width 3000
> height 2600

> hide #!22 models

> show #!23 models

> show #!7 models

> hide #!7 models

> show #16 models

> hide #16 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!7 models

> hide #!8 models

> show #!8 models

> show #16 models

> hide #!7 models

> show #!9 models

> show #10 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> select #7, #8

Expected an objects specifier or a keyword  

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> hide sel & #10#!8-9 cartoons

> select clear

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> transparency (#!23 & sel) 60

> select clear

> select #21

23 models selected  

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> lighting full

> lighting simple

> lighting full

> graphics silhouettes false

> lighting shadows false

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> select clear

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> show sel cartoons

> select clear

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> transparency (#!23 & sel) 0

> select clear

> save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
> height 2600

> hide #16 models

> show #!15 models

> hide #!8 models

> hide #!9 models

> hide #10 models

> show #!7 models

> hide #!23 models

> color #15.2 #663399b4 models

> color #15.3 #7b5d99b4 models

> color #15.4 #6495edb4 models

> select clear

> save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
> height 2600

> hide #!15 models

> show #!1 models

> color #1 #b2b2b2b4 models

> hide #!1 models

> show #!15 models

> select clear

> nucleotides #!7 atoms

> style nucleic & #!7 stick

Changed 0 atom styles  

> splitss

Unknown command: splitss  

> cartoon style coil thickness 0.25

> hide #!15 models

> cartoon style coil thickness 1.25

> cartoon style coil thickness 1

> cartoon style coil thickness 1.25

> cartoon style sheet thickness 1.25

Expected an atoms specifier or a keyword  

> cartoon style ribbon thickness 1.25

Expected an atoms specifier or a keyword  

> show #!15 models

> hide #!15 models

> cartoon style ribbon thickness 10

Expected an atoms specifier or a keyword  

> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> cartoon style ribbon thickness 1.25

Expected an atoms specifier or a keyword  

> cartoon style coil thickness 1.25

> cartoon style nucrib thickness 1.25

Expected an atoms specifier or a keyword  

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> licorice

> show #!15 models

> view

> color #15.9 #ff0000b4 models

> color #15.8 #7dcdd2b4 models

> hide #!15.2 models

> show #!15.2 models

> hide #!15 models

> select #7/C:66

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #7/C:66

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #7/C:66

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #7/C:65

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #7/C:69

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> style #!7 sphere

Changed 5662 atom styles  

> style #!7 stick

Changed 5662 atom styles  

> hide #!7 atoms

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15.2 models

> hide #!15.3 models

> hide #!15.1 models

> show #!15.1 models

> hide #!15.1 models

> show #!15.1 models

> hide #!15.1 models

> view

> show #!15.1 models

> hide #!15.1 models

> show #!15.1 models

> color #15.1 #b2b2b2b2 models

> color #15.1 #b2b2b2b4 models

> undo

[Repeated 9 time(s)]

> show #!15.1 models

> color #15.1 #b2b2b2b4 models

> show #!15.2 models

> show #!15.3 models

> show #!23 models

> hide #!23 models

> hide #!15 models

> show #!15 models

> color #15.6 #ffffffb4 models

> color #15.7 #ffd700b4 models

> color #15.5 #ff00ffb4 models

> color #16 #663399b4

> color #16 rebeccapurple

> show #16 models

> hide #16 models

> show #16 models

> hide #16 models

> show #16 models

> hide #!15 models

> hide #!7 models

> color #16 rebeccapurple

[Repeated 1 time(s)]

> select clear

> select #16/A

1652 atoms, 1694 bonds, 223 residues, 1 model selected  

> color sel #663399ff

> select clear

> select #16/B

1616 atoms, 1650 bonds, 211 residues, 1 model selected  

> color sel #7b5d99ff

> select clear

> show #!23 models

> hide #!23 models

> show #!23 models

> show #!7 models

> hide #!7 models

> show #!8 models

> show #!9 models

> show #10 models

> show #!15 models

> hide #!23 models

> show #!7 models

> hide #16 models

> hide #!15 models

> show #!15 models

> hide #10 models

> hide #!9 models

> hide #!7 models

> hide #!8 models

> hide #!15 models

> show #!2 models

> show #!8 models

> color #2 #b2b2b2b4 models

> undo

[Repeated 1 time(s)]

> hide #!2 models

> show #!17 models

> hide #!17.1 models

> show #!17.1 models

> color #17.1 #b2b2b2b4 models

> color #17.2 #6495edb4 models

> color #17.3 #ff00ffb4 models

> color #17.4 #ffffffb4 models

> color #17.5 #ffd70005 models

> color #17.5 #ffd700b4 models

> color #17.6 #7dcdd2b4 models

> color #17.7 #ff0000b4 models

> color #17.8 #778899b4 models

> color #17.9 #ff69b4b4 models

> color #17.10 #36558fb4 models

> color #17.11 #98a8c5b4 models

> select clear

[Repeated 1 time(s)]

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> show sel & #!8 cartoons

> select clear

> show #!15 models

> show #!7 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!7 models

> save C:\Users\David/Desktop/new-snaps/test.png supersample 4 width 3000
> height 2600

> show #!23 models

> hide #!17 models

> hide #!17.1 models

> show #!17.1 models

> hide #!17 models

> show #!17 models

> hide #!23 models

> show #!15 models

> show #!23 models

> hide #!23 models

> hide #!17 models

> hide #!8 models

> show #!7 models

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
> 3000 height 2600

> color #15.2 #66339978 models

> color #15.3 #7b5d9978 models

> color #15.4 #6495ed78 models

> color #15.5 #ff00ff78 models

> color #15.6 #ffffff78 models

> color #15.7 #ffd70078 models

> color #15.8 #7dcdd278 models

> color #15.9 #ff000078 models

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-1.png supersample 4 width
> 3000 height 2600

> color #15.2 #6633998c models

> color #15.3 #7b5d998c models

> color #15.4 #6495ed01 models

> color #15.4 #6495ed8c models

> color #15.5 #ff00ff8c models

> color #15.6 #ffffff8c models

> color #15.7 #ffd7008c models

> color #15.8 #7dcdd28c models

> color #15.9 #ff000077 models

> color #15.9 #ff00008c models

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-140.png supersample 4
> width 3000 height 2600

> hide #!15 models

> hide #!7 models

> show #!8 models

> show #!2 models

> hide #!2 models

> show #!15 models

> show #!23 models

> hide #!23 models

> show #!21 models

> hide #!21 models

> hide #!15 models

> show #!17 models

> color #17.2 #6495ed8c models

> color #17.3 #ff00ff8c models

> color #17.4 #ffffff8c models

> color #17.5 #ffd7008c models

> color #17.6 #7dcdd28c models

> color #17.7 #ff0000b3 models

> color #17.7 #ff00008c models

> color #17.8 #7788998c models

> color #17.9 #ff69b48c models

> color #17.10 #36558f8c models

> color #17.11 #98a8c58c models

> select clear

> show #!15 models

> hide #!15 models

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
> width 3000 height 2600

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 0.75

> licorice

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
> width 3000 height 2600

[Repeated 1 time(s)]

> graphics silhouettes color black width 3

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
> width 3000 height 2600

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> show sel & #!8 atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140.png supersample 4
> width 3000 height 2600

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-140-1.png supersample 4
> width 3000 height 2600

> show #!15 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> hide #!15 models

> hide #!8 models

> show #!15 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> hide #!15 models

> show #!23 models

> save C:\Users\David/Desktop/new-snaps/5J44.png supersample 4 width 3000
> height 2600

> show #!7 models

> hide #!7 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!15 models

> show #!1 models

> hide #!1 models

> show #!7 models

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
> 3000 height 2600

> hide #!7 models

> show #!8 models

> hide #!15 models

> show #!17 models

> save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4.png supersample 4 width
> 3000 height 2600

> hide #!17 models

> show #!18 models

> hide #!8 models

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4.png supersample 4 width
> 3000 height 2600

> color #18.2 #6495ed8c models

> color #18.3 #ff00ff8c models

> color #18.4 #ffffff8c models

> color #18.5 #ffd7008c models

> color #18.6 #7dcdd28c models

> color #18.7 #ff00008c models

> color #18.8 #7788998c models

> color #18.9 #ff69b48c models

> color #18.10 #ecb0e18c models

> color #18.11 #f7dff38c models

> show #!8 models

> hide #!8 models

> show #!9 models

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-transp.png supersample 4
> width 3000 height 2600

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> show sel & #!9 cartoons

> select clear

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> show sel & #!9 atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-40_Fig4-transp.png supersample 4
> width 3000 height 2600

> hide #!18 models

> show #!17 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> color #17.2 cornflowerblue models

[Repeated 1 time(s)]

> color #17.2 #6495ed02 models

> color #17.2 cornflowerblue models

[Repeated 1 time(s)]

> color #17.3 #ff00ff8d models

> color #17.3 magenta models

> color #17.4 white models

> color #17.4 #fffffffe models

> color #17.4 white models

> color #17.5 gold models

[Repeated 1 time(s)]

> color #17.6 #7dcdd2ff models

[Repeated 1 time(s)]

> color #17.7 red models

[Repeated 1 time(s)]

> color #17.8 lightslategrey models

[Repeated 1 time(s)]

> color #17.9 hotpink models

[Repeated 1 time(s)]

> color #17.10 #36558fff models

> color #17.10 #36558ffe models

> color #17.10 #36558fff models

> color #17.11 #98a8c5ff models

[Repeated 1 time(s)]

> color #17.1 #b2b2b2ff models

[Repeated 1 time(s)]

> color #17.2 #6495edfe models

> color #17.2 cornflowerblue models

> save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4-no-transp.png supersample
> 4 width 3000 height 2600

> color #17 #b2b2b2fe models

> color #17 #b2b2b2ff models

> undo

[Repeated 2 time(s)]

> color #17 #b2b2b2ff models

> close #17

> show #!8 models

> show #!2 models

> color #2 #b2b2b2ff models

> ui tool show "Color Zone"

> color zone #2 near #8 distance 5.57

> volume splitbyzone #2

Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 0 as #17.1, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 1 as #17.2, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 2 as #17.3, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 3 as #17.4, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 4 as #17.5, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 5 as #17.6, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 6 as #17.7, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 7 as #17.8, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 8 as #17.9, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 9 as #17.10, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  
Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc 10 as #17.11, grid
size 320,320,320, pixel 0.928, shown at level 1.13, step 1, values float32  

> hide #!17 models

> show #!17 models

> show #!18 models

> hide #!18 models

> hide #!17 models

> show #!17 models

> hide #!8 models

> save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4.png supersample 4 width
> 3000 height 2600

> show #!8 models

> color #17.2 #6495edb4 models

> color #17.2 #6495ed8c models

> color #17.3 #ff00ff8c models

> color #17.4 #ffffff8c models

> color #17.5 #ffd7008c models

> color #17.6 #7dcdd28c models

> color #17.7 #ff00008c models

> color #17.8 #77889991 models

> color #17.8 #7788998c models

> color #17.9 #ff69b48c models

> color #17.10 #36558f8c models

> color #17.11 #98a8c58c models

> save C:\Users\David/Desktop/new-snaps/EatA-15_Fig4_transp.png supersample 4
> width 3000 height 2600

> show #!15 models

> hide #!17 models

> hide #!8 models

> show #!7 models

> color #15.1 #b2b2b2ff models

> color #15.2 rebeccapurple models

> color #15.3 #7b5d99ff models

> color #15.2 #663399fe models

> color #15.2 rebeccapurple models

> color #15.4 cornflowerblue models

> color #15.4 #6495edfe models

> color #15.4 cornflowerblue models

> color #15.5 magenta models

[Repeated 1 time(s)]

> color #15.6 white models

[Repeated 1 time(s)]

> color #15.7 gold models

[Repeated 1 time(s)]

> color #15.8 #7dcdd2ff models

[Repeated 1 time(s)]

> color #15.9 red models

[Repeated 1 time(s)]

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-notransp.png supersample
> 4 width 3000 height 2600

> close #15

> show #!1 models

> color #1 #b2b2b2ff models

> color zone #1 near #7 distance 5.57

> volume splitbyzone #1

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 0 as #15.1, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 1 as #15.2, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 2 as #15.3, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 3 as #15.4, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 4 as #15.5, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 5 as #15.6, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 6 as #15.7, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 7 as #15.8, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  
Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc 8 as #15.9, grid
size 320,320,320, pixel 0.928, shown at level 0.642, step 1, values float32  

> hide #!7 models

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4.png supersample 4 width
> 3000 height 2600

> color #15.2 #6633998c models

> color #15.3 #7b5d998c models

> color #15.1 #b2b2b28c models

> color #15.4 #6495ed8c models

> color #15.5 #ff00ff8c models

> color #15.6 #ffffff8c models

> color #15.7 #ffd7008c models

> color #15.8 #7dcdd28c models

> color #15.9 #ff00008c models

> show #!7 models

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> show sel & #!7 atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-25_Fig4-tranps.png supersample 4
> width 3000 height 2600

> hide #!15 models

> hide #!7 models

> show #10 models

> show #!21 models

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> show sel & #10 cartoons

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #10 models

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
> 3000 height 2600

> show #10 models

> color #21.1 #b2b2b28c models

> color #21.2 #2c514c02 models

> color #21.2 #2c514c8c models

> color #21.3 #6ea0988c models

> color #21.4 #6495ed8c models

> color #21.5 #ff00ff8c models

> color #21.6 #ffffff8c models

> color #21.7 #ffd7008c models

> color #21.8 #7dcdd28c models

> color #21.9 #ff00008c models

> color #21.10 #7788998c models

> color #21.11 #ff69b48c models

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
> width 3000 height 2600

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> show sel & #10 atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
> width 3000 height 2600

> close #21

> show #!4 models

> volume #4 level 10.16

> hide #!4 models

> show #!4 models

> hide #10 models

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
> 3000 height 2600

> hide #!4 models

> show #!4 models

> color zone #13 near #10 distance 12.16

> volume splitbyzone #13

Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 4.3, step 1, values float32  

> hide #!4 models

> hide #!19 models

> show #!19 models

> close #19

> show #!13 models

> volume #13 level 5.725

> show #10 models

> hide #10 models

> color zone #13 near #10 distance 12.16

> volume splitbyzone #13

Opened EatA-G12_composite_map.ccp4 gaussian 0 as #19.1, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 1 as #19.2, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 2 as #19.3, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 3 as #19.4, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 4 as #19.5, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 5 as #19.6, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 6 as #19.7, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 7 as #19.8, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 8 as #19.9, grid size 356,356,356,
pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 9 as #19.10, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  
Opened EatA-G12_composite_map.ccp4 gaussian 10 as #19.11, grid size
356,356,356, pixel 0.86, shown at level 5.72, step 1, values float32  

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4.png supersample 4 width
> 3000 height 2600

> show #10 models

> color #19.1 #b2b2b28c models

> color #19.2 #2c514c8c models

> color #19.3 #6ea098fe models

> color #19.3 #6ea09801 models

> color #19.3 #6ea0988c models

> color #19.4 #6495ed8c models

> color #19.5 #ff00ff8c models

> color #19.6 #ffffff8c models

> color #19.7 #ffd7008c models

> color #19.8 #7dcdd28c models

> color #19.9 #ff00008c models

> color #19.10 #7788998c models

> color #19.11 #ff69b48c models

> select clear

> save C:\Users\David/Desktop/new-snaps/EatA-G12_Fig4-transp.png supersample 4
> width 3000 height 2600

> hide #!19 models

> hide #10 models

> show #!11 models

> show #!22 models

> hide #!22 models

> show #!20 models

> hide #!11 models

> save C:\Users\David/Desktop/new-snaps/SepA-40_Fig4.png supersample 4 width
> 3000 height 2600

> show #!11 models

> color #20.1 #b2b2b28c models

> color #20.2 #6495ed8c models

> color #20.3 #ff00ff8c models

> color #20.4 #ffffff8c models

> color #20.5 #ffd7008c models

> color #20.6 #7dcdd28c models

> color #20.7 #ff00008c models

> color #20.8 #7788998c models

> color #20.9 #ff69b4fe models

> color #20.9 #ff69b48c models

> color #20.10 #ecb0e18c models

> color #20.11 #f7dff38c models

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> show sel & #!11 atoms

> save C:\Users\David/Desktop/new-snaps/SepA-40_Fig4-transp.png supersample 4
> width 3000 height 2600

> hide #!20 models

> show #!22 models

> hide #!11 models

> show #!12 models

> hide #!22 models

> show #!14 models

> volume #14 level 0.05935

> close #22

> color zone #14 near #12 distance 18.16

> volume splitbyzone #14

Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 0 as #21.1,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 1 as #21.2,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 2 as #21.3,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 3 as #21.4,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 4 as #21.5,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 5 as #21.6,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 6 as #21.7,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 7 as #21.8,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 8 as #21.9,
grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1, values
float32  
Opened Pic-40_cryosparc_P7_J1193_002_volume_map_sharp.mrc gaussian 9 as
#21.10, grid size 320,320,320, pixel 0.938, shown at level 0.0593, step 1,
values float32  

> hide #!21 models

> hide #!12 models

> show #!21 models

> save C:\Users\David/Desktop/new-snaps/Pic-40.png supersample 4 width 3000
> height 2600

> show #!12 models

> color #21.1 #b2b2b28c models

> color #21.2 #6495ed8c models

> color #21.3 #ff00ff8c models

> color #21.4 #ffffff8c models

> color #21.5 #7dcdd28c models

> color #21.6 #ff00008c models

> color #21.7 #7788998c models

> color #21.8 #ff69b48c models

> color #21.9 #ecb0e18c models

> save C:\Users\David/Desktop/new-snaps/Pic-40-tranps.png supersample 4 width
> 3000 height 2600

> color #21.10 #f7dff38c models

> select #7,8,9,10,11/A:78,106,211

117 atoms, 107 bonds, 15 residues, 5 models selected  

> select #12/A:72,100,203

15 atoms, 12 bonds, 3 residues, 1 model selected  

> show sel atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/Pic-40-tranps.png supersample 4 width
> 3000 height 2600

> hide #!21 models

> show #!23 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #10 models

> show #!11 models

> hide #!7 models

> show #16 models

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> hide sel & #10#!8-9,11-12 cartoons

> hide sel & #10#!8-9,11-12 atoms

> select clear

> save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
> height 2600

> hide #!11 models

> hide #!12 models

> save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
> height 2600

> save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
> height 2700

> save C:\Users\David/Desktop/new-snaps/overlay.png supersample 4 width 3000
> height 2600

> hide #!23 models

> select #7,8,9,10,11,12/A

35524 atoms, 36127 bonds, 49 pseudobonds, 4880 residues, 11 models selected  

> show sel & #10#!8-9 cartoons

> select clear

> hide #!8 models

> hide #!9 models

> hide #10 models

> hide #16 models

> show #!7 models

> show #!15 models

> hide #!15 models

> save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
> height 2700

> show #!15 models

> hide #!15.3 models

> hide #!15.2 models

> hide #!15.1 models

> save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
> height 2700

[Repeated 2 time(s)]

> hide #!15 models

> hide #!7 models

> show #!8 models

> show #!17 models

> hide #!17.11 models

> hide #!17.10 models

> save C:\Users\David/Desktop/new-snaps/15-1.png supersample 4 width 3000
> height 2700

> hide #!17 models

> hide #!8 models

> show #!9 models

> show #!18 models

> hide #!18.11 models

> hide #!18.10 models

> save C:\Users\David/Desktop/new-snaps/40-1.png supersample 4 width 3000
> height 2700

> hide #!18 models

> hide #!9 models

> show #10 models

> show #!19 models

> hide #!19.10 models

> show #!19.10 models

> hide #!19.3 models

> hide #!19.2 models

> save C:\Users\David/Desktop/new-snaps/G12-1.png supersample 4 width 3000
> height 2700

> hide #!19 models

> show #!19 models

> hide #!19 models

> hide #10 models

> show #!9 models

> show #!8 models

> hide #!9 models

> show #!17 models

> save C:\Users\David/Desktop/new-snaps/15-1.png supersample 4 width 3000
> height 2700

[Repeated 1 time(s)]

> hide #!17 models

> hide #!8 models

> show #!9 models

> show #!18 models

> save C:\Users\David/Desktop/new-snaps/40-1.png supersample 4 width 3000
> height 2700

> hide #!18 models

> hide #!9 models

> show #!7 models

> show #!15 models

> save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
> height 2700

> view

> save C:\Users\David/Desktop/new-snaps/25-1.png supersample 4 width 3000
> height 2700

> hide #!15 models

> hide #!7 models

> show #10 models

> hide #10 models

> show #!9 models

> show #!18 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit.cxs

——— End of log from Sun Nov 2 23:30:54 2025 ———

opened ChimeraX session  

> hide #!9 models

> hide #!18 models

> show #10 models

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/composite_map_J1626+J1599+J1295.ccp4

Opened composite_map_J1626+J1599+J1295.ccp4 as #4, grid size 356,356,356,
pixel 0.86, shown at level 1.85, step 2, values float32  

> volume #4 step 1

> volume #4 level 10.77

> volume #4 level 11

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/EatA-FabG12_RSR_real_space_refined_013.pdb

Chain information for EatA-FabG12_RSR_real_space_refined_013.pdb #22  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #!22 models

> show #!22 models

> select #22

8934 atoms, 9092 bonds, 28 pseudobonds, 1172 residues, 2 models selected  

> color (#!22 & sel) #55ffffff

> color (#!22 & sel) #ffffffff

> hide #!4 models

> select clear

> hide #10 models

> show #10 models

> show #!4 models

> color #4 #b2b2b2b4 models

> hide #10 models

> select #22/A:1-256

1600 atoms, 1633 bonds, 6 pseudobonds, 210 residues, 2 models selected  

> color (#!22 & sel) cornflower blue

> select clear

> select #22/A:78,106,211

24 atoms, 22 bonds, 3 residues, 1 model selected  

> color sel magenta

> select clear

> select #22/A:481-560

151 atoms, 149 bonds, 1 pseudobond, 19 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel gold

> select clear

> select #22/A:611-629

117 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected  

> color (#!22 & sel) #7dcdd2ff

> select #22/A:669-699

185 atoms, 182 bonds, 3 pseudobonds, 27 residues, 2 models selected  

> color (#!22 & sel) #ff0000ff

> select #22/A:781-794

51 atoms, 52 bonds, 1 pseudobond, 7 residues, 2 models selected  

> color (#!22 & sel) #778899ff

> color (#!22 & sel) #ff69b4ff

> select #22/B

1586 atoms, 1627 bonds, 3 pseudobonds, 208 residues, 2 models selected  

> color (#!22 & sel) #2c514cff

> select #22/C

1567 atoms, 1600 bonds, 3 pseudobonds, 202 residues, 2 models selected  

> color (#!22 & sel) #6ea098ff

> select clear

> ui tool show "Color Zone"

> color zone #4 near #22 distance 5.16

> hide #!22 models

> color zone #4 near #22 distance 6.67

> color zone #4 near #22 distance 5.6

> color zone #4 near #22 distance 4.84

> graphics silhouettes width 1

> save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-2.png supersample 4
> width 500 height 500

[Repeated 2 time(s)]

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/cryosparc_P6_J1626_007_volume_map_sharp.mrc

Opened cryosparc_P6_J1626_007_volume_map_sharp.mrc as #24, grid size
356,356,356, pixel 0.86, shown at level 0.0179, step 2, values float32  

> volume #24 step 1

> volume #24 level 0.06059

> hide #!4 models

> show #!4 models

> volume #24 level 0.0747

> hide #!24 models

> hide #!4 models

> show #!4 models

> save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-2.png supersample 4
> width 500 height 500

> hide #!4 models

> show #!24 models

> color zone #24 near #22 distance 5.16

> color zone #24 near #22 distance 5.53

> color #24 #b2b2b2ff models

> color zone #24 near #22 distance 5.53

> color zone #24 near #22 distance 4.88

> save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-consens.png supersample
> 4 width 500 height 500

> hide #!24 models

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-
> MAP/J1599/J1599-resampled/cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc

Opened cryosparc_P6_J1599_004_volume_map_sharp_resampled.mrc as #25, grid size
356,356,356, pixel 0.86, shown at level 0.0252, step 2, values float32  

> show #!4 models

> volume #25 step 1

> volume #25 level 0.2254

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> color #25 #b2b2b2ff models

> color zone #24 near #22 distance 4.91

> color zone #25 near #22 distance 5.16

> color zone #25 near #22 distance 4.88

> save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-loc-1.png supersample 4
> width 500 height 500

> hide #!25 models

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/J1295/cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc

Opened cryosparc_P6_J1295_002_volume_map_sharp_resampled.mrc as #26, grid size
356,356,356, pixel 0.86, shown at level 0.0291, step 2, values float32  

> volume #26 step 1

> volume #26 level 0.1905

> show #!4 models

> volume #26 level 0.2291

> hide #!4 models

> color #26 #b2b2b2ff models

> color zone #25 near #22 distance 4.85

> color zone #26 near #22 distance 5.16

> color zone #26 near #22 distance 5.39

> color zone #26 near #22 distance 5.04

> save C:\Users\David/Desktop/new-snaps/EMDB/EatA-G12-loc-2.png supersample 4
> width 500 height 500

> volume #26 level 0.23

> volume #26 level 0.229

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit.cxs

——— End of log from Sun Nov 16 18:26:26 2025 ———

opened ChimeraX session  

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #10 models

> hide #10 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #16 models

> hide #16 models

> show #!17 models

> hide #!1 models

> hide #!26 models

> show #!17.10 models

> show #!17.11 models

> hide #!17 models

> show #!18 models

> show #!18.10 models

> show #!18.11 models

> hide #!18 models

> show #!19.2 models

> show #!19.3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> show #!4 models

> hide #!19 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> show #!13 models

> hide #!13 models

> show #!5 models

> hide #!4 models

> show #!4 models

> select #4

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-0.14988,0,1,0,-3.7143,0,0,1,-3.0634

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99843,0.053725,-0.015885,-4.5976,-0.053323,0.99827,0.024706,1.0648,0.017185,-0.02382,0.99957,-2.5236

> view matrix models
> #4,0.99867,-0.036628,0.036363,-0.56328,0.036145,0.99925,0.013864,-11.278,-0.036844,-0.012531,0.99924,4.3952

> ui tool show "Fit in Map"

> fitmap #4 inMap #5

Fit map composite_map_J1626+J1599+J1295.ccp4 in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 80208 points  
correlation = 0.3463, correlation about mean = 0.1333, overlap = 1.079e+05  
steps = 176, shift = 4.02, angle = 2.47 degrees  
  
Position of composite_map_J1626+J1599+J1295.ccp4 (#4) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99760209 -0.02760094 0.06346856 -9.70153389  
0.02472356 0.99865001 0.04568259 -14.87071002  
-0.06464377 -0.04400387 0.99693773 13.51873268  
Axis -0.54386119 0.77687675 0.31729722  
Axis point 210.45522440 0.00000000 177.83322647  
Rotation angle (degrees) 4.72960394  
Shift along axis -1.98696477  
  

> select clear

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!22 models

> ui tool show Matchmaker

QWindowsWindow::setGeometry: Unable to set geometry 640x574+880+428 (frame:
658x621+871+390) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 638x566+881+435 (frame: 656x613+872+397)
margins: 9, 38, 9, 9 minimum size: 486x321 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=626, y=448)))  

> matchmaker #!22 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker SepA-Fab40_RSR_real_space_refined_208.pdb, chain A (#11) with EatA-
FabG12_RSR_real_space_refined_013.pdb, chain A (#22), sequence alignment score
= 2568.8  
RMSD between 531 pruned atom pairs is 1.321 angstroms; (across all 745 pairs:
2.371)  
  

> select clear

> fitmap #22 inMap #4

Fit molecule EatA-FabG12_RSR_real_space_refined_013.pdb (#22) to map
composite_map_J1626+J1599+J1295.ccp4 (#4) using 8934 atoms  
average map value = 16.96, steps = 64  
shifted from previous position = 0.164  
rotated from previous position = 0.494 degrees  
atoms outside contour = 2766, contour level = 11  
  
Position of EatA-FabG12_RSR_real_space_refined_013.pdb (#22) relative to
composite_map_J1626+J1599+J1295.ccp4 (#4) coordinates:  
Matrix rotation and translation  
0.99999997 0.00016736 -0.00019720 0.00453544  
-0.00016737 0.99999998 -0.00005185 0.02561694  
0.00019719 0.00005188 0.99999998 -0.03116835  
Axis 0.19660280 -0.74754244 -0.63445065  
Axis point 153.18392184 0.00000000 21.46109238  
Rotation angle (degrees) 0.01511415  
Shift along axis 0.00151670  
  

> select clear

> hide #!22 models

> show #!22 models

> ui tool show "Color Zone"

> color zone #4 near #22 distance 4.84

> volume splitbyzone #4

Opened composite_map_J1626+J1599+J1295.ccp4 0 as #27.1, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 1 as #27.2, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 2 as #27.3, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 3 as #27.4, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 4 as #27.5, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 5 as #27.6, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 6 as #27.7, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 7 as #27.8, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 8 as #27.9, grid size 356,356,356,
pixel 0.86, shown at level 11, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 9 as #27.10, grid size
356,356,356, pixel 0.86, shown at level 11, step 1, values float32  

> color #27.10 #6ea098b4 models

> color #27.9 #2c514cb4 models

> color #27.8 #ff69b4b4 models

> color #27.7 #ff0000b4 models

> color #27.6 #7dcdd2b4 models

> color #27.5 #ffd700b4 models

> hide #!27.4 models

> show #!27.4 models

> color #27.4 #ffffffb4 models

> color #27.3 #ff00ffb4 models

> color #27.2 #6495edb4 models

> color #27.1 #b2b2b208 models

> color #27.1 #b2b2b2b4 models

> hide #!27.1 models

> show #!27.1 models

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

> licorice

> select clear

> hide #!27 models

> show #!27 models

> hide #!27.9 models

> hide #!27.10 models

> hide #!27 models

> show #!27 models

> hide #!27.1 models

> show #!27.1 models

> hide #!27.1 models

> show #!27.1 models

> show #!27.9 models

> show #!27.10 models

> graphics silhouettes width 4

> save C:\Users\David/Desktop/new-snaps/test4.png supersample 4 width 3000
> height 2600

> show #!4 models

> hide #!4 models

> volume gaussin #4 sd 1

Expected a density maps specifier or a keyword  

> volume gaussian #4 sDev 1

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #28, grid size
356,356,356, pixel 0.86, shown at step 1, values float32  

> hide #!27 models

> volume #28 level 5.995

> show #!27 models

> color #28 #b2b2b2b4 models

> volume #28 level 6.455

> hide #!27 models

> color zone #28 near #22 distance 5.16

> color zone #28 near #22 distance 6.01

> volume splitbyzone #28

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 as #29.1, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 as #29.2, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 as #29.3, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 as #29.4, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 as #29.5, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 as #29.6, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 as #29.7, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 as #29.8, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 as #29.9, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 as #29.10, grid size
356,356,356, pixel 0.86, shown at level 6.45, step 1, values float32  

> color #29.10 #6ea098b4 models

> color #29.9 #2c514cb4 models

> color #29.8 #ff69b4b4 models

> color #29.7 #ff0000b4 models

> color #29.6 #7dcdd2b4 models

> color #29.5 #ffd700b4 models

> color #29.4 #ffffffb4 models

> color #29.3 #ff00ffb4 models

> color #29.2 #6495edb4 models

> color #29.1 #b2b2b2b4 models

> hide #!29.9 models

> hide #!29.10 models

> show #!29.9 models

> show #!29.10 models

> save C:\Users\David/Desktop/new-snaps/test4.png supersample 4 width 3000
> height 2600

> hide #!29 models

> hide #!22 models

> show #!17 models

> show #!8 models

> save C:\Users\David/Desktop/new-snaps/test5.png supersample 4 width 3000
> height 2600

> hide #!8 models

> hide #!17 models

> show #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!23 models

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit2.cxs

——— End of log from Mon Nov 17 16:44:16 2025 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #16 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!28 models

> hide #!28 models

> show #!22 models

> show #!17 models

> hide #!17 models

> show #!8 models

> show #!9 models

> select #8/A

6266 atoms, 6372 bonds, 8 pseudobonds, 829 residues, 2 models selected  

> select #8/A #9/A #22/A

17860 atoms, 18152 bonds, 37 pseudobonds, 2360 residues, 6 models selected  

> hide sel cartoons

> hide #!23 models

> show #!23 models

> hide #!22 models

> show #!22 models

> show #!28 models

> hide #!28 models

> hide #16 models

> show #16 models

> select #8/B,C #9/B,C #16/A,B #22/B,C

12634 atoms, 12934 bonds, 16 pseudobonds, 1656 residues, 7 models selected  

> show sel surfaces

> transparency (#!8-9,16,22 & sel) 90

> select clear

> show #!28 models

> hide #!28 models

> show #!28 models

> show #!15 models

> hide #!15 models

> hide #!28 models

> show #!17 models

> hide #!16 models

> show #!16 models

> hide #!8 models

> hide #!9 models

> show #!18 models

> show #!28 models

> show #!15 models

> hide #!16 models

> hide #!15 models

> show #10 models

> hide #10 models

> show #!1 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume mask #1 surfaces #16

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked as #30, grid
size 78,80,66, pixel 0.928, shown at step 1, values float32  

> hide #!28 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> volume #30 level 0.5583

> hide #!22 models

> show #!22 models

> show #!29 models

> hide #!30 models

> show #!30 models

> hide #!22 models

> show #!22 models

> hide #!30 models

> show #!30 models

> hide #!29 models

> show #!29 models

> hide #!22 models

> show #!22 models

> volume mask #29 surfaces #22

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 0 masked as #31, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 1 masked as #32, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 2 masked as #33, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 3 masked as #34, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 4 masked as #35, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 5 masked as #36, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 6 masked as #37, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 7 masked as #38, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 8 masked as #39, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  
Opened composite_map_J1626+J1599+J1295.ccp4 gaussian 9 masked as #40, grid
size 84,78,83, pixel 0.86, shown at step 1, values float32  

> hide #!22 models

> hide #!31 models

> hide #!32 models

> hide #!33 models

> hide #!34 models

> hide #!35 models

> hide #!36 models

> hide #!37 models

> hide #!38 models

> hide #!39 models

> hide #!40 models

> show #!40 models

> show #!39 models

> close #31-40

> show #!28 models

> volume mask #28 surfaces #22

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #31, grid size
84,78,83, pixel 0.86, shown at step 1, values float32  

> volume #31 level 5.226

> color #31 #b2b2b2ff models

> select clear

> close #31

> show #!27 models

> hide #!27 models

> show #!4 models

> hide #!4 models

> volume gaussian #4 sDev 2

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #31, grid size
356,356,356, pixel 0.86, shown at step 1, values float32  

> volume #31 level 6.321

> volume #31 level 2.736

> volume mask #31 surfaces #22

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #32, grid size
84,78,83, pixel 0.86, shown at step 1, values float32  

> volume #32 level -0.265

> close #32

> close #31

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/composite_map_J1626+J1599+J1295.ccp4

Opened composite_map_J1626+J1599+J1295.ccp4 as #31, grid size 356,356,356,
pixel 0.86, shown at level 1.85, step 2, values float32  

> volume #31 step 1

> volume #31 level 17.64

> select clear

> select #31

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #31,0.99663,-0.081706,0.0071854,10.201,0.081724,0.99665,-0.0023133,-11.764,-0.0069724,0.0028927,0.99997,0.69415

> ui tool show "Fit in Map"

> fitmap #31 inMap #5

Fit map composite_map_J1626+J1599+J1295.ccp4 in map
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc using 38473 points  
correlation = 0.3863, correlation about mean = 0.09089, overlap = 8.407e+04  
steps = 236, shift = 6.51, angle = 5.32 degrees  
  
Position of composite_map_J1626+J1599+J1295.ccp4 (#31) relative to
SepA-40_cryosparc_P7_J1169_009_volume_map_sharp.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99748278 -0.02886231 0.06476929 -9.64591594  
0.02591303 0.99860886 0.04592236 -15.11779553  
-0.06600461 -0.04412839 0.99684305 13.79263787  
Axis -0.53613713 0.77859142 0.32611713  
Axis point 210.99850006 0.00000000 174.51925630  
Rotation angle (degrees) 4.81743578  
Shift along axis -2.10103676  
  

> select clear

> volume gaussian #31 sDev 2

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian as #32, grid size
356,356,356, pixel 0.86, shown at step 1, values float32  

> volume #32 level 5.17

> show #!22 models

> color #32 #ffb2b2b4 models

> select #22

8934 atoms, 9092 bonds, 28 pseudobonds, 1172 residues, 2 models selected  

> hide sel surfaces

> volume #32 level 3.948

> volume #32 level 1.505

> volume #32 level 0.1262

> volume #32 level 0.5648

> select #22/B,C

3153 atoms, 3227 bonds, 6 pseudobonds, 410 residues, 2 models selected  

> show sel surfaces

> volume mask #32 surfaces #22

Opened composite_map_J1626+J1599+J1295.ccp4 gaussian masked as #33, grid size
84,78,83, pixel 0.86, shown at step 1, values float32  

> select clear

> hide #!22 models

> color #33 #ffb2b2ff models

> volume #33 level 0.1293

> close #33

> volume #32 level 2.288

> close #32

> show #!22 models

> hide #!22 models

> volume mask #31 surfaces #22

Opened composite_map_J1626+J1599+J1295.ccp4 masked as #32, grid size 84,78,83,
pixel 0.86, shown at step 1, values float32  

> hide #!32 models

> show #!32 models

> volume #32 level 12.48

> volume gaussian #32 sDev 1

Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #33, grid size
84,78,83, pixel 0.86, shown at step 1, values float32  

> volume #33 level 4.866

> volume #33 level 6.086

> volume gaussian #32 sDev 2

Opened composite_map_J1626+J1599+J1295.ccp4 masked gaussian as #34, grid size
84,78,83, pixel 0.86, shown at step 1, values float32  

> hide #!33 models

> volume #34 level 2.789

> show #!17 models

> show #!18 models

> show #!7 models

> show #!8 models

> hide #!17 models

> hide #!18 models

> hide #!8 models

> hide #!7 models

> show #!8 models

> show #!9 models

> show #!17 models

> show #!18 models

> hide #!9 models

> hide #!8 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> hide #!17 models

> hide #!18 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> show #!8 models

> show #!9 models

> volume mask #2 surfaces #8

Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked as #35, grid
size 65,50,86, pixel 0.928, shown at step 1, values float32  

> volume mask #3 surfaces #9

Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked as #36, grid
size 65,49,89, pixel 0.928, shown at step 1, values float32  

> hide #!8 models

> hide #!9 models

> select #23

7500 atoms, 7628 bonds, 1006 residues, 1 model selected  

> transparency (#!23 & sel) 90

> select clear

> volume #30 level 0.5205

> volume gaussian #30 sDev 1

Opened EatA-25_cryosparc_P18_J417_007_volume_map_sharp.mrc masked gaussian as
#37, grid size 78,80,66, pixel 0.928, shown at step 1, values float32  

> volume #37 level 0.2599

> volume #37 level 0.3494

> volume #37 level 0.5661

> volume gaussian #35 sDev 1

Opened EatA-15_cryosparc_P7_J1177_008_volume_map_sharp.mrc masked gaussian as
#38, grid size 65,50,86, pixel 0.928, shown at step 1, values float32  

> volume gaussian #36sd 1

Missing or invalid "volumes" argument: only initial part "#36" of atom
specifier valid  

> volume gaussian #36 sDev 1

Opened EatA-40_cryosparc_P7_J1175_008_volume_map_sharp.mrc masked gaussian as
#39, grid size 65,49,89, pixel 0.928, shown at step 1, values float32  

> volume #38 level 0.5776

> volume #39 level 0.7292

> volume #37 level 0.5317

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit2.cxs

> volume #38 color #36558f

> volume #39 color #ecb0e1

> select clear

> volume #37 color rebeccapurple

> volume #33 color #2c514c

> volume #33 level 8.306

> ui tool show "Color Zone"

> color zone #33 near #22 distance 5.16

> show #!7 models

> hide #!7 models

> hide #!23 models

> show #!16 models

> show #!23 models

> select #16/B

1616 atoms, 1650 bonds, 211 residues, 1 model selected  

> color (#!16 & sel) #7b5d99ff

> select clear

> hide #!16 models

> color zone #37 near #16 distance 5.57

> color #33 #6ea098ff models

> select clear

> color #37 #7b5d99ff models

> select clear

> volume #33 level 10.09

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit2.cxs

——— End of log from Wed Nov 26 13:25:16 2025 ———

opened ChimeraX session  

> hide #!37 models

> hide #!38 models

> hide #!39 models

> hide #!33 models

> show #!7 models

> hide #!7 models

> show #!8 models

> show #!9 models

> show #10 models

> hide #10 models

> show #!11 models

> hide #!11 models

> show #!16 models

> transparency #8-9,16,23#!29 0

> select #8 #9 #16

21560 atoms, 21994 bonds, 25 pseudobonds, 2844 residues, 5 models selected  

> hide sel surfaces

> hide #!23 models

> show #!23 models

> select clear

> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-FabG12/ACTUAL-
> FINAL-MAP/EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb

Chain information for EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb #40  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show Matchmaker

> matchmaker #!40 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker EatA-FabG12_RSR_real_space_refined_010.pdb, chain A (#10) with
EatA-FabG12_RSR_real_space_refined_227-coot-0.pdb, chain A (#40), sequence
alignment score = 3231.2  
RMSD between 747 pruned atom pairs is 0.372 angstroms; (across all 762 pairs:
0.770)  
  

> licorice

> select #40/A

5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> select #40/B

1690 atoms, 1735 bonds, 1 pseudobond, 221 residues, 2 models selected  

> color (#!40 & sel) #2c514cff

> select clear

> select #40/C

1572 atoms, 1613 bonds, 209 residues, 1 model selected  

> color sel #6ea098ff

> select clear

> save C:\Users\David/Desktop/high_res_image-COMPLEX.png supersample 4 width
> 3000 height 2200

[Repeated 1 time(s)]

> hide #!40 models

> show #!40 models

> hide #!40 models

> show #!40 models

> save C:\Users\David/Desktop/high_res_image-COMPLEX.png supersample 4 width
> 3000 height 2200

[Repeated 1 time(s)]

> hide #!40 models

> hide #!16 models

> hide #!9 models

> hide #!8 models

> save C:\Users\David/Desktop/high_res_image-5J44.png supersample 4 width 3000
> height 2200

> show #!40 models

> show #!28 models

> hide #!28 models

> show #!29.1 models

> show #!29.2 models

> show #!29.3 models

> show #!29.4 models

> show #!29.5 models

> show #!29.6 models

> show #!29.7 models

> show #!29.8 models

> show #!29.9 models

> show #!29.10 models

> hide #!23 models

> select #40/A

5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected  

> show sel cartoons

> select #40/A

5781 atoms, 5865 bonds, 22 pseudobonds, 762 residues, 2 models selected  

> color (#!40 & sel) #ffffffff

> select #40/A:1-256

1600 atoms, 1633 bonds, 6 pseudobonds, 210 residues, 2 models selected  

> color (#!40 & sel) cornflower blue

> select clear

> select #40/A:78,106,211

24 atoms, 22 bonds, 3 residues, 1 model selected  

> color sel magenta

> select clear

> select #40/A:481-560

151 atoms, 149 bonds, 1 pseudobond, 19 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel gold

[Repeated 1 time(s)]

> select clear

> select #40/A:611-629

117 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color (#!40 & sel) #7dcdd2ff

> select #40/A:669-699

185 atoms, 182 bonds, 3 pseudobonds, 27 residues, 2 models selected  

> color (#!40 & sel) #ff0000ff

> select clear

> hide #!29.10 models

> hide #!29.9 models

> ui tool show "Side View"

> save C:\Users\David/Desktop/high_res_image-COMPLEX-ZOOM.png supersample 4
> width 3000 height 2200

[Repeated 1 time(s)]

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_Fig4-edit2.cxs

——— End of log from Wed Dec 10 17:24:00 2025 ———

opened ChimeraX session  

> view

> hide #!29 models

> show #!29 models

> hide #!29 models

> hide #!40 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #10 models

> show #!11 models

> show #!12 models

> show #!39 models

> hide #!39 models

> hide #10 models

> show #10 models

> show #!40 models

> show #!1 models

> hide #!1 models

> close #10

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!13 models

> hide #!13 models

> show #!15 models

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!23 models

> hide #!23 models

> show #!24 models

> hide #!24 models

> show #!24 models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!26 models

> hide #!26 models

> show #!27 models

> hide #!27 models

> rename #1 id #50

> rename #2 #8 #17 #35 id #1

> hide #!1.2 models

> show #!1.2 models

> hide #!7 models

> hide #!9 models

> hide #!11 models

> hide #!12 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1 models

> show #!1 models

> show #!1.1 models

> hide #!1.1 models

> rename #3 #9 #18 #36 #39 id #2

> show #!2.4 models

> hide #!2.4 models

> show #!2.5 models

> hide #!2.5 models

> show #!2.5 models

> hide #!2.5 models

> show #!2.4 models

> hide #!2.4 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.3 models

> show #!2.2 models

> hide #!2.2 models

> show #!2.1 models

> hide #!2.1 models

> rename #7 #15 #16 #30 #37 #50 id #3

> show #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.5 models

> hide #!3.5 models

> rename #4 id #50

> show #!50 models

> close #22

> rename #27-34 id #51

> rename #51.1 id #52

> rename #51.2 id #53

> rename #51.3 id #54

> rename #51.4 id #55

> rename #51.5 id #56

> rename #51.6 id #57

> rename #51.7 id #58

> close #51

> rename #50 #40 #13 #19 #24 #25 #26 #52-58 id #4

> hide #!4.1 models

> hide #!4.2 models

> show #!4.2 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.4 models

> hide #!4.4 models

> show #!4.5 models

> hide #!4.5 models

> show #!4.6 models

> hide #!4.6 models

> show #!4.7 models

> hide #!4.7 models

> show #!4.8 models

> hide #!4.8 models

> show #!4.9 models

> hide #!4.9 models

> show #!4.10 models

> hide #!4.10 models

> show #!4.11 models

> hide #!4.11 models

> show #!4.12 models

> hide #!4.12 models

> show #!4.13 models

> hide #!4.13 models

> show #!4.14 models

> hide #!4.14 models

> show #!2.2 models

> rename #5 id #50

> rename #50 #11 #20 id #5

> show #!5.2 models

> show #!38 models

> hide #!38 models

> close #38

> rename #6 id #50

> rename #50 #12 #14 #21 id #6

> show #!6.1 models

> hide #!6.1 models

> show #!6.2 models

> show #!23 models

> hide #!23 models

> rename #1 EatA-15

> rename #2 EatA-40

> rename #3 EatA-25

> rename #4 EatA-G12

> rename #5 SepA-40

> rename #6 Pic-40

> rename #23 id #7

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-maps-
> aligned_1.cxs includeMaps true

——— End of log from Wed Jan 7 13:06:56 2026 ———

opened ChimeraX session  

> close #1.1

> close #1.3-4

> close #2.1

> close #2.3-5

> close #3.2-6

> close #4.1

> close #4.3-14

> close #5.1

> close #5.3

> close #6.1

> close #6.3-4

> show #!7 models

> hide #!7 models

> select #2/A

5813 atoms, 5915 bonds, 7 pseudobonds, 769 residues, 2 models selected  

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show sel atoms

> hide sel atoms

> show sel cartoons

> select clear

> hide #!2.2 models

> show #!2.2 models

> hide #!2 models

> hide #!5.2 models

> show #!5.2 models

> show #!2 models

> select #5/A

6163 atoms, 6259 bonds, 6 pseudobonds, 830 residues, 2 models selected  

> show sel cartoons

> select clear

> hide #!5.2 models

> hide #!2 models

> select #6/A

5739 atoms, 5840 bonds, 14 pseudobonds, 828 residues, 2 models selected  

> show sel cartoons

> select clear

> show #!5.2 models

> show #!2 models

> select clear

> select #2/A

5813 atoms, 5915 bonds, 7 pseudobonds, 769 residues, 2 models selected  

> ui tool show Matchmaker

> select #2/A #5/A #6/A

17715 atoms, 18014 bonds, 27 pseudobonds, 2427 residues, 6 models selected  

> matchmaker #!5.2#!6.2 & sel to #2.2 & sel

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#2.2) with
SepA-Fab40_RSR_real_space_refined_208.pdb, chain A (#5.2), sequence alignment
score = 3055  
RMSD between 762 pruned atom pairs is 0.490 angstroms; (across all 768 pairs:
1.177)  
  
Matchmaker EatA-Fab40_RSR_real_space_refined_206.pdb, chain A (#2.2) with Pic-
Fab40_RSR_real_space_refined_199.pdb, chain A (#6.2), sequence alignment score
= 1978.2  
RMSD between 643 pruned atom pairs is 0.933 angstroms; (across all 689 pairs:
1.962)  
  

> select clear

> save C:/Users/David/Documents/lab/Berndsen/EatA/AAA_final-sessions/all-
> models.cxs includeMaps true

——— End of log from Wed Jan 7 13:23:09 2026 ———

> view name session-start

opened ChimeraX session  
Desktop color scheme is dark  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: Z17H000CGLL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 7 days, 9 hours, 55 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: V5K6P7RJ2X
          Display Firmware Version: Version 17.0 (Build 21A329)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: NNQ2Q230MJ
          Display Firmware Version: Version 17.0 (Build 21A329)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (0)

Note: See TracTickets for help on using tickets.